Why don't you call them and explain your situation? As in, I mailed my seat deposit, but I am concerned that it may have been lost in the mail. Then ask them what you can do. Maybe you can arrange to have them fax you a new acceptance letter, which you can then sign and mail off OVERNIGHT with a new check. Then stop payment on the check you already wrote. And make sure that you can track your new acceptance stuff via the USPS website. Personally, I had mine sent with delivery confirmation or return receipt (I forget what it's called) so that I got a postcard back once Syracuse got my acceptance stuff.
I wouldn't worry, you can call the school and I'm sure they'll be happy to arrange to take your money. After all, they admitted you, so they obviously want you to come.