The short version of my issue at hand,
Found a solution that modifies the android.bat to allow you to start and run the android sdk and avd manager on the x64 jdk. So far I've been able to start it updating, but I don't know what other implications running the emulator and compiling against the x64 jdk will have.
http://code.google.com/p/android/issues/detail?id=3917
good luck.