Yes. In preferences, change the ports used by Mac aMule. Then, have the router forward these ports, which are different than those used by eMule on Windows, to the Mac.
So, the end result: router forwards eMule ports to the Windows machine and forwards aMule ports to the Mac.
However, you probably don't really want to be running eMule/aMule *simultaneously* on both machines. They will compete for bandwidth. You will be splitting your credits. Etc.