Are you saying that you got a letter from the IRS (like a CP2000) reporting that you owe tax from a prior year?
The process of handling these "letter audits" (as the IRS calls them) is separate from the e-filing and refund process.
This means that while the IRS has the right to take any refund to pay any money that you owe, they won't until the letter audit process is completed (you have to reply to this letter, correct?) by which point your refund from your already e-filed return will have probably already arrived to you.
But in a sense, you don't "owe" the money yet, because you haven't written back (they usually give you about three weeks to reply) confirming that you accept their change to the return - by which point you are very likely to have your refund. Give it another week - and be sure to answer that letter in a timely fashion - even if you can't pay it yet, the worst thing in the world is to NOT reply to an IRS letter.