In fact you can :-) After the boot up with PPC card in, just install WarpUP software, and everything should be ok.
However, with Mediator in there as well, it might be better just to install from scratch. Just install OS3.1, the libraries for te 68k CPU and you can continue from there.
-EDIT-
Oops, saw you didn't have a Mediator afterall, so just plug the card in, boot the computer and install WarpUP, and start replacing libraries, datatypes and whatever with PPC ones.
