First let me start out by saying that I have never had anything stolen off my bike and never had a bike stolen or even messed with. Well, there was one time some drunk urinated in the muffler and on the rear wheel but I'll bet even odds that the guy was so drunk that he thought he was pissing on a really strangely shaped shiny tree.
How much of this experience is good luck and how much is because of the precautions I take is anyone's guess. I know that most other touring riders that I've talked to have had pretty much the same experience as I've had. My guess is that a lot of my good luck has to do with the fact that I tend to stay away from heavily populated areas and that I typically ride sportbikes which are generally less desirable to thieves. My precautions probably also play a relatively small part.
Security is where your touring style and type of luggage intersect. The two main security considerations are the security of yout gear and belongings while they are on your bike and the security of the bike itself.
When I first started touring I just tied various canvas bags to the back seat. Later, as I got more money, I bought some soft saddlebags and a tank bag. For most of the years I've been touring I have used various kinds and styles of soft luggage. The only exception ot this was for the four yeaars I owned a Kawasaki Concours. The Connie came with hard saddle bags. Even on the Connie I had to add tail packs or other types of soft luggage because the hard bags weren't big enough.
All things considered there are a lot of advantages to soft luggage. The only real disadvantage is that they offer almost no security to your belongings.
The way I deal with this problem is pretty simplistic but it works. My general rule is that I am never out of sight of the bike when any soft luggage is mounted. This system works just fine fine as long as you don't want to leave your bike for more than a few seconds but it can put a big crimp in your style if you want to wander on foot. Since I seldom sightsee it isn't a problem.
If I really want to sightsee I get a motel room in the area, stash my luggage there, and then wander with the bike naked except for a tank bag. I empty my tank bag of everything but the map and maybe rain gear and then take the bag with me as I wander. A small back pack to carry the tank bag or tank bag rigged with extra straps so that it can be worn as a backpack makes it a lot easier to take your tank bag with you.
As for your jacket and helmet, you can either take them with you or secure them to the bike. I have heard of people stealing a helmet by cutting the chin strap on a helmet secured to a bike's helmet lock. It makes no sense to me to do that as it ruins the helmet but it does happen. A better, but still risky, solution is to get a small cable lock and loop it through the sleeve of the jacket and the eye opening in the helmet. This only works for full face helmets. Then, lock the whole mess to the bike--preferably with the lock under the seat. This still leaves you vulnerable to vandals and a determined thief.
For soft luggage that is closed with zippers or some strap systems you can use either cable ties or purpose made luggage locks to secure both the zippers (or strap fasteners or whatever) and the bag's attach point on the bike. If you use cable ties a thief will need tools or a knife (to cut the cable ties) to get into the bags or remove them from the bike. The problem is that you'll also need tools to get into the bags. If you use cable ties, you'll also have to bring a bunch of cable ties. This isn't that big a deal as cable ties are pretty cheap and don't take a lot of space but still, it's one more thing to bring and keep track of.
This will not stop a determined thief or serious vandal, but will stop a casual thief. Purpose built luggage locks are available in luggage stores or the travel section of some stores like Target.
The only sure-fire solution is to use lockable hard luggage and never leave the bike without locking everthing inside the luggage. This may not be an option for you because of time, price, or availability for your bike.
For security when eating, I only eat in places where I can see my bike. Since I almost always eat my meals (and sleep for that matter) in small towns this is pretty easy rule to follow. In most small town cafes you can almost always park where you can see your bike. If you can't it's not that big a deal as there are often so few people around that there is not really any need for security. Still, I'm a bit paranoid and never let my bike out of sight when eating.
What you do depends on what type of thief you're trying to stop. There are essentially two types of thief: the professional and the opportunist. Pros want the bike to sell or breakdown for parts to sell. Opportunist sometimes want the bike for themselves but usually want a free ride for a while.
There isn't really much you can do to prevent the determined professional except not own the type of bike they're looking for or hiding the bike so that they don't know it's there to be stolen. Professionals usually don't even try to start the bike. They just pick it up, put it in a truck, and haul it away. The really good ones can do this in seconds and make almost no noise.
Professional thiefs are usually looking for specific bikes. The most commonly stolen bike these days is any non-Sportster Harley-Davidson. These are stolen for either resale or chop-shops and from what I've read mostly are stolen by pros. Sportbikes can be stolen by pros in urban areas but are mostly stolen by opportunists in both urban and rural areas. Standards and dual sports are seldom stolen and when they are it is the opportunist. As near as I can tell BMW's are almost never stolen.
The most secure thing you can do for your bike is get a high strength chain and lock your bike to an immovable object like a light post, building support (concrete or steel, not wood), a big tree, or the like. The next best is to lock your bike to another bike with such a chain. Even with this precaution a well equipped pro will still get your bike. Chains of this type (something that takes a torch or extreme power cutting tools to get through) are very heavy and it's usually not practical to bring something like this on a trip.
If you don't secure your bike to something immovable, there's really nothing you can do to prevent someone from simply picking up your bike and dumping it in the back of a truck. Actually, there is one thing--put your bike in your room. Some people actually do this. I think that it's a very rude and nasty thing to do to a motel owner.
If you can't make the bike immovable the next best thing is to make it so that the bike cannot be pushed. This can often stop the opportunist. The choices are a chain or cable lock, a high strength U lock, or a disk lock. I have heard that it's possible to defeat these locks with liquid nitrogen but can't say for sure.
Opportunistic thieves often will punch out the ignition switch, hot wire the engine and ride away. If you're electrically inclined you can install a hidden cutoff switch. I used to do this years ago. The easiest place to put the switch is in series with the engine cutoff switch. It's best to place the hiden switch under the seat or somewhere where you can use it without it being obvious to an observer that you're doing something unusual. It does no good to have a hidden switch that someone knows is there.
There are also alarms. I looked into these but decided that they were too much trouble. If I did get an alarm I'd be sure to get one with a motion detector and a remote pager. I'd install it such that it wasn't obvious that there was an alarm on the bike. Pros know how to disable many alarms and will do so if they know it's there. I would only put an alarm on a high risk bike like a Harley.
I use a simple disk lock and have used that for about ten years. Before that I didn't really do anything. A couple years ago I bought a disk lock with a built-in motion detector alarm. This seems like a reasonable compromise between size, weight, and functionality. I'm not entirely happy with the alarm on this lock. Its sensitivity seems to be pretty inconsistent. It's sometimes impossible to install or remove the lock without setting off the alarm for a fraction of a second. Sometimes I can kick the front tire and it won't go off. Still, I think that it's better than an ordinary disk lock.
I always cover my bike for the night. I use a black nylon cover made by EZ Tour. This cover is black and made of coated rip-stop nylon. It packs very small, smaller that any other cover I've seen, and is waterproof too. I got black because it sort of helps camouflage the bike.
I used to try and hide the bike and still do if it's not too far out of the way. If I can park in a shadow with a black cover the bike's almost imvisible. Otherwise I try to park as close to my room as possible. In reality this probably doesn't matter for me as I am a really deep sleeper. If an alarm went off I would never hear it. Hell, anything short of war wouldn't wake me up. Still, it makes me feel better.
If the motel has a 24 hour desk and you ask real nice, sometimes the clerk will let you park outside the door where the clerk can keep an eye on it. I'm not sure they really watch but it probably can't hurt.
I try to stay in small motels in small towns. I would never stay in a Motel 6 or any other place that caters to the absolute bottom of the price sprectrum. There are just too many strange people staying at those places. In many cases the small town family owned motel is cheaper and they are a lot more secure.