I've been living healthier since January, and have noticed a reasonable loss of weight since then, and am also seeing muscles I didn't know I had. But one thing that plagues me is a nice big plot of fat on my stomach, and some residual on my obliques/love handles. With my stomach cleaner and my pecs a little tighter I think I'd be at a nice stopping point. Are certain problem areas inherent in genetics, as going to a family gathering would seem to suggest? I'm trying to get a little leaner in the next two weeks, getting to a decent shape before school starts again; you know, first impressions are standards and all. So, standing plan is 1 hour of cardio a day, with pec/arm exercises cycling with rest of body on alternating days. Should that fill my problem in nicely?

The problem- Where your body tends to store fat more- Could be genetic. To lose the fat, you need to work on your nutrition and your cardio- Post something about your average daily diet in the nutrition forums, you're sure to get lots of help there in that area. When it comes to cardio, sounds like you're doing quite a bit- Use the search option to look up guerilla cardio, it's helped a lot of people on this site, and is probably more efficient than what you're doing now-
As for the rest of your program, I'm not too sure what you mean-

with pec/arm exercises cycling with rest of body on alternating days. Should that fill my problem in nicely?

Do you work your entire body on alternating days, but do pecs and arms every day with your cardio? If you could post your weekly routine in the critique my training forum, again, more help will be on the way.