I'm going to paint my TKO tunnel patch with POR-15 paint and I wanted to know if I put the seam sealer on before or after the paint. I was going to do two coats so should I put it on after the frist coat.

Depends on what kind of paint you are going to use.

If it were me... I would epoxy with 2 coats, then use the seam sealer. The reason is the epoxy will keep out all the bad stuff. If you seam seal and then epoxy, you don't get any corrosion protection.