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Edit: Resolved, thanks for the responses guys!

Well, they're going to get something in the mail, so you clearly need to explain that part. Just write a brief e-mail to the admissions office and they'll figure it out.

-edit- Resolved!

bryang91 wrote:Problem #1 - I don't want to hurt my application, so I don't want to anger the adcomms with a paper application (because they prefer electronic applications, right). I would call and tell them to disregard my paper application, but I already sent in a check.

What should I do?

They don't prefer it to such an extent that they're going to trash your application because of it. If you're a good applicant who helps their numbers, they're not going to deny you just because it's slightly inconvenient to deal with a hard copy. Just call the admissions office and explain. They presumably extended the deadline because they're hurting for applicants, so they're not in a position to turn strong candidates away for this kind of shit.