Can you put Thompson's water seal over latex paint?

You will want to either prep-sand the wood, or apply a chemical prep, available at a paint store.

The wood is now classed as sealed. You need, as pointed out to sand the surface use a 120 grit sandpaper then wipe fully to remove the dust, it is then the job of the undercoat to make a base for the final coat. This is important as you will need an OIL BASED undercoat. Water based will not help you and will not adhere correctly. The reason for the undercoat as well is to help the colour definition of the top coat. Its assuming that the wood is going to be outside (as it was water proofed initially) . If this is the case use a good exterior grade top coat or it will whether very quickly