Applying effects in waveform, carried over to multitrack

They shouldn't be! What should happen (although I haven't tested this recently) if you do that is that a warning should pop up, asking you whether you want to save the changes you made to the wav files. If you don't save the changes, then the files will be as they were when placed in the multitrack session, before you did anything to them. Multitrack is only a very posh file player, and by default it just plays what you load. So if you don't save the changes, then the effects simply won't be there, as the files will still be in their raw state.