I have 2 payments left on a payment plan from last year. Will they take the rest out of my return this year or should I continue with my payment plan?

Well, this is a bit tricky.  The IRS will tell you to keep making payments until you are notified otherwise.  However, in almost all cases, they will retain your refund against any back taxes you owe.

To avoid late fees, I would probably keep making payments until I get a letter or statement telling me not to, even if that meant sending in an extra payment (it will eventually be returned).  If you have can check your payment balance online you might be able to see if your refund was applied to it.  Or, stop making payments and take the risk that, if something goes wrong with your tax refund, they may hit you with a penalty.