MPF, you should be able to answer this.
Will gaining muscle, in say my chest, arms, and shoulders, help at all with my stomach?
Will it contour my body and help make my stomach flatter, or do you need to do separate workouts for your stomach? I'm not talking about a six pack, just making my stomach more flat (getting rid of fat).
Yes absolutely. You can't actually "focus" on your stomach and expect to slim down. Situps and ab work outs don't burn any more fat than the calories you use to do the workout. Only intense, full body workouts burn significant amounts of fat. Training the muscles in your stomach does the same thing training any muscle does; it makes them bigger. Now, it's good to train the muscles in your stomach (especially in your obliques, on the sides) because you want a strong core and you want the muscles to show through when you slim down, but you also don't want to over train your abs (as so many guys do) because than you get that bulging gut where the guy has abs, but it's not a good looking flat stomach, but a bunch of protruding muscles.
Either way, training the rest of your body is not only going to help trim your waist, it's actually going to be more effective. Unfortunately, things like arms and shoulders are secondary muscle groups; they'll still help, for sure, and they should be worked, but engaging larger muscles like your quads (squats, lunges or leg press), lats (rows, pulls, etc.) and chest will burn more calories and help you trim faster. The larger the muscles you're working, the more hormones your body also release and, in the case of weight training, the hormones triggered are ones that promote muscle growth and increase metabolism and testosterone production, both of which promote fat loss. What you should do is develop a basic regimen, even if it's only 3 days a week and precede or conclude each workout with ~20 minutes of cardio, or even power walking.
But absolutely, gaining muscle anywhere is going to promote some fat loss; just adding more muscle to your composition forces your body to burn calories at a higher rate. Add in the calories burned while exercising those muscles and make smart dietary choices - as in, still get the burger and fries when you're out with your friends, but grab some fruit instead of chips at home, or water instead of soda - and you'll trim up quickly. It's a lot easier than most people think; 75% of the battle is the willpower to do it. The other 25% is the knowledge of what to do. Also, adding muscle in your chest, shoulders, arms and back will make your waist look more trim because of the proportions of your body changing. That, along with the calories burned from weight lifting (which burns fat at a higher rate than cardio, FYI) will do wonders for making you look more slender and muscular.
A decent starter routine with three days a week, and a rest day in between each would be:
Monday:
Flat bench press (barbell or dumb bells)
Incline press (barbell or dumb bells)
Cable flies: 2 sets decline, 2 sets slight incline, 2 sets deep incline
Dumb bell curls
Two-hand cable curls
Woodcutters (cable exercise for abs/obliques)
Tuesday: Rest
Wednesday:
Lat pull down
Seated row
Bent over dumb bell row
Skullcrushers
Two-hand cable tricep extensions
Decline situps (with a 10lb plate or medicine ball, if it's easy)
Thursday: Rest
Friday:
Military press (seated)
Upright cable row
Deltoid raises (cable or dumbell)
Front dumbell raises
Roman chair crunches
Leg press
Leg extensions
Saturday & Sunday Rest
Do cardio before or after each work out. 5 minutes to warm up, 15 minutes of decent work, and 2.5 minutes to cool down should be more than enough. It's up to you when you do it; if you're trying to build muscle, they recommend doing it before you lift and if you're trying to tone they recommend doing it after you lift. I like doing it after I lift just because I think it takes away from my energy with the weights if I run first. You can also decide to not do cardio at all on your lift days and instead do 30 minutes on the days you don't lift. Either way works. This should be a pretty easy routine to get into though; it doesn't require much expertise and you can look up all of the lifts on youtube to get an idea for the form. I left out anything that's dangerous or complex like squats and compound lifts so that it would be accessible for someone whose getting acquainted with lifting. Scott Herman's gym videos on youtube are good instruction and motivation.