(Another) Tech Isolation Transformer grounding question
If you want to use the isolation transformer as intended then both secondary wires should remain free from earth. The result will be that if "one" secondary side comes in contact with earth you still have no risk of electrocution.

This also means that you are free to use 2 or 3 prong connectors and there is no need to change this. I still recommend however to mark your outlets comming from the transformer so that it is clear that neutral and live are floating with respect to earth