I just took apart my bike (threaded headset), had it repainted, got a new headset installed, greased the steerer tube, and now I am trying to stick the stem back in, but it seems incredibly hard. Am I suppose to loosen the top screw of the headset? Or do I just push really hard and freak that my stem might be getting scratched to the bajebus!

By 'headset' do you mean the quill stem? The bolt that secures the wedge at the bottom of a quill stem should be loose enough to slide the stem into the steer tube. If it got tightened for some reason while out, this may explain why it won't go back in easily. The 'top screw' on a threaded headset only adjusts the headset, and should have no effect on inserting the quill stem.

No, the wedge bolt is not tightened... Do I just need to push and wiggle it in?

If only there were a slippery substance that might be helpful when two pieces of metal need to slide past each other...

(but for the record, it shouldn't have to be forced. so look everything over again...)