How does paying federal taxes late affect my 2008 rebate?
I know for sure that if you send your return in, without a check for what you owe, the IRS will send you a bill for that amount. I did that a couple times when I didn’t have the money immediately available. I got the bill sometime in June, as I recall, sent the money in, no problem. You need to send the money in, when you get the bill. Concerning the rebate and your other questions, I would call the IRS.
Here is the IRS FAQ page relative to the stimulus package. Note that the answer to your question about withholding your 2007 taxes due from your stimulus check is near the bottom of the page.