i used to do that (before i had to send the emu off for repair). i routed the waldorf pulse through the inputs and then through different filters/effects depending on what key was pressed. and it worked brilliantly.
i don't know what the problem with your setup is though. you could off course just use the rfx compressor to make it louder or maybe your signal is just low in volume. sorry for stating the obvious

mind you, the pulse is an awfully loud synth so maybe that's why i never had that problem.