I believe the transfer application is mail-only. The pdf of last year's application is posted on the MIT transfer website here: Transfer Application | MIT Admissions
As the page says, the fall 2013 app will be posted around September.
As for your classes, I'm also in CS. Likewise, my situation is comparable to yours because I'm a rising freshman at a small liberal arts school, and they want me to take all sorts of humanities classes. Here's the best advice I can give you: Don't underestimate the power of negotiation. I haven't even started my freshman year yet, and I'm already signed into a calc-based physics class (offered only to junior physics majors at my school) because I talked with the professor and had to do a bit of weaseling to get around scheduling conflicts. So, talk with your professors, explain the situation, show real passion for your subjects, and see if you can get placed in the chem, calc, bio and physics classes MIT recommends.