Is it possible that I can make payments to pay the fees off because the IRS had kept my refund this year?

How did you choose to pay your fees?

It was suppose to have been deduced from my federal tax.

If that's what you chose unfortunately I don't think you can change it, but you can always contact the IRS to see if they are able to work something out with you! Here's their phone number 1.800.829.1040