Yep, if you owe the IRS the check will go towards it, you won't receive one.
Also, if you want to set up a payment plan there is a form to fill out and you can arrange how much you want to pay each month. I did this with my husbands business. We have ours directly taken from a bank account just for this purpose. If you know how much you owe, definately do that because the longer you wait the more penalty you'll have to pay.
http://www.irs.gov/pub/irs-pdf/f9465.pdf