Why do I weigh presumably so low, but look big-ish? How can I get a flat stomach?

Wait. You're a guy? And 98 lbs? AND 5'6"? That is really skinny... You should work on gaining weight, not losing it. Unfortunately, there is no real way to do spot weight loss, except of course for surgery. If you gain weight in some places, that's how it is. You can't make your body lose weight in the area you want it to by exercising it. Your body gains and loses weight in areas that are determined by genes. I would say that you really can't be so bad as you seem to think though. Some body fat is a good thing anyway; it's unhealthy to have no fat on you. Either way, at 98 lbs. it can't be that much.