I owed additioanl taxes in 2015. I set up a payment plan and are current on my payments. I'm getting a refund on my 2016 taxes. I mailed a check to pay off the IRS for th

Timing is everything.  If the IRS gets the check and applies it to your account before they work on your return, you should get a refund as your account would be paid in full.  However, if the IRS does not get and apply your payment before they work on your refund, your refund will be used to pay the balance owed.  The good thing is that, once they post the check to the account, if they held back a part of your refund, they will return the excess of the amount to you.  You will not lose, however, it may take time for all this to be resolved, if the refund is processed first.