You would have to call the IRS and ask them to apply the over payment to your current tax liability. Probably the easiest thing to do is let them send you a check, deposit it, and then use the funds to pay them. As for the miscellaneous deductions, it sounds like the program is telling you that you would need $985 of Miscellaneous expense for it to be worth claiming them. That would be due to the fact that in order to take a deduction they must exceed 2% of your Adjusted Gross Income (AGI) and then you can only deduct the portion that exceeds that 2% floor.
