how to use set false path properly to constrain clocks in different clock domains

You shouldn't need to use the set_false_path command, the clock groups features should be enough. Timequest isn't supposed to analyse timing between asynchronous clock groups. Try adding the PLL clock in another group.

I don't remember the exact command but you can ask Timequest to reparse your sdc constraints file. See if you have any warning about ignored commands or clocks not found when it executes your sdc commands.