Well to put in my input (I miss working out heavily, I used to be able and allowed to, but due to the severity of this flare, most of the time I'm not up to it, and I'm also instructed not to)....I have been in a bodybuilding lifestyle for 4 plus years. A pure gym rat. I was doing great, deadlifting 405, put on lots of muscle, etc...learned a lot of advanced info.....Crohns and bodybuilding go together like Diarrhea and laxatives....you need to rely mostly on diet to get what you want out of bodybuilding...
To clarify on some stuff Jeff said, you can either build muscle, or lose it, there's no shaping, toning, or any "bulking". It either builds (hypertrophy) or deteriorates (atrophy or, in true deterioration, you have dystrophy, such as Muscular Dystrophy...). So, lifting heavy will not get you too "bulky", as you simply are building the fibers of your muscles (or creating new ones, which is termed "hyperplasia" I believe). So if you already have trouble gaining weight/muscle due to this disease or genetics making it difficult, you shouldn't do any "high reps", as they're useless in most cases. Rep ranges of 5-12 reps, depending on the muscle, will get you what you want as far as growth. The way you determine what reps you should go for, is the bigger the muscle the, the fewer reps in general, it takes to cause muscle tearing (on a microscopic level, that's what you want). For example, big muscle groups are chest, back, legs (quads, hams, glutes)...small would be biceps, triceps, shoulders, calves....You can work out more than 3 times a week, that's fine, but you have to make sure each muscle is getting rest. Experienced lifters will alternate groups so you can let one heal while you pummel another.
For example, here's a good one I followed for a while at one point:
Mon-Upper body pushing (bench press, military press, incline bench, and tri's)
Tues-Lower Body pushing (squats, leg press, leg extensions, calves)
Wed-OFF (rest)
Thurs-Upper body pulling (Pulldowns, rows, shrugs, lats and biceps)
Fir-Lower body pulling (Hamstring curls, deadlifts, Stiff legged deadlifts)
Sat-Off
Sun-Cardio and abs
This routine was a mass gaining one for me, all sessions took around 45 minutes, and sets varied, the bigger the muscle, the more sets I'd do, and less reps per set. For example, biceps (the arm related ones, you actually have "biceps" in your leg too) would be perhaps a 10 rep set, done 3 sets on Thursday of my above plan, but that same day, because the lats are huge muscles, I'd do 5 sets on them, but each set would be 5-9 reps.
You don't need to switch up a workout that's working still, your body will learn to adapt to things (after all building muscle is adapting, the body is preparing for heavier work loads, because you are stressing the muscles to do more), but only switch up a good plan if it stalls things. And DO NOT start out heavy until you learn each movement.
Diet is key though, and if you're flaring, that throws a monkey in the wrench. Depending on what your bowels will tolerate, you should shoot for 1 gram of protein per lb of bodyweight if possible, twice that to three times that for carbs, and fill in the rest of the space with healthy fats as best you can to get to the correct calorie level. You may need to adjust your caloric intake as you go, just try for example 3000 cals a day and see if you gain, static, or lose. This way you can gauge where your Total Caloric Burn (TCB) is, as nobody can tell you this unless you get tests done, or through trial and error. Go for around 1 gallon of water a day (about 3-4 liters) if possible. Space out meals as evenly as possible, but make sure you time them around your workouts well, so you can get maximum results after each session. Get a high dose of quick digesting carbs with quick protein following a workout....gatorade in a protein shake is perfect, and cheap, and fast.
Creatine is hit or miss with it's "irritation" of the GI tract, some can take it with IBD, others not at all. I'm fine with it as long as I'm not flaring, but I've been flaring for 10 months. Carnitine is an amino like you said, but it's generally not that effective to warrant it's cost, because it's usually expensive. And like Jeff said you're trying to gain muscle, if you take Carnitine you will use up valuable calories. Your body will not add much muscle at all if you're in a deficit, so calories are needed to be in excess. Muscle is costly for the body to keep around, so if your body is going to add it, you need to show it it doesn't need to worry about the cost (in calories) to have it. If your body always has excess, it'll get the message that you can afford to add muscle, as your eating enough to fuel it's maintenance. As for weight gainers, many are loaded with simple sugars to get a bomb of calories, real food is always better though, even if you can tolerate a weight gainer.
And to clarify what Jeff said also, you cannot turn fat into muscle, that is impossible biologically, but you can create the appearance that that is happening when you workout heavily, as that will often burn fat and build muscle. The problem is, you really should focus on one or the other. As only a newbie or somebody on steroids will be able to trim significant fat AND add significant muscle (you're a newbie so it'll happen for a while to start) all at the same time. So pick a goal, do one or the other. That's why bodybuilders have "bulking" phases and "cutting" phases. You try to catch 2 rabbits at the same time and both will get away.
When you say "bloated" I'm guessing your talking about abdominal fat, or a slight beer belly....that will slowly go away in time, you're weight for 5'11" is quite low, so your body will react well to a weight/muscle gaining regimen. Let the belly go away on it's own, besides, if you add mass to the rest of it, it'll make the belly less noticable. Big muscular guys can carry fat well because they have the muscle to "blend it in".
There's so much to tell you to start. This is only the surface of it, and I'm probably forgetting some crucial details, but I know I've covered some good basics. About going "to failure" (which is lifting in a set until you fail trying to go for another rep), that should be used, but used sparingly, as you can overtrain if you do it on every set. Try to do it on maybe half your sets, the last half (you don't want to totally exhaust your body in the first half of your workout).
I wrote an enormous beginners guide somewhere a couple years ago, I'll try and find it. I started a facebook group for Crohns bodybuilders, but it's not fully up and running yet. I've trained with some big guys (not as a partner all the time though). Sam Urbach was 2004 Mr. Illinois, and Bill Norberg was 1982 Mr. Collegiate America. Awesome dudes. If you can get an experienced partner, they can help you learn the ropes on site.
One last important thing (I really don't want to overwhelm you), make sure you learn proper forms on each movement first, if you don't know already. Injury will do you no good, and may affect your IBD.
I'll come back here later to speak of some more basics when I get time, as I honestly mean it, this is only the tip of the iceberg, there's a lot of science to this as Jeff will know.
