Eureka ~! Figured I would post the solution here so nobody else has to suffer the trauma I've put myself through. The solution was actually very simple.
Make 2 copies of the U64 emulator Rename them so you can tell them apart u64emu.exe and u64emu2.exe(It actually states this in the Readme, but I must have missed it). To launch the games, simply go to the command line and type ..."your path to the executable file/u64emu.exe - auto".....note...This DOES NOT WORK WITH PLATINUM EDITION.
From What i have gathered on my mythical journeys throughout various forums, to get it to work with platinum edition would require some sort of wrapper, If anyone knows where to find one of them, that would be helpful, as it is beyond my capabilities at the moment.
Hope this helps, feel free to post any related questions here.
P.S. This is one of the best forums I've ever been to. So much knowledge, so little B.S.