What doesn't work? You almost certainly don't need to compile Arduino from source. You probably just need to replace the RXTX library that comes with it with a version that's compiled for 64-bit processors (which you might be able to find a package for). You might need to compile the Arduino version of avrdude from source, but that won't require checking out the whole (huge) Arduino source tree, just downloading: http://www.arduino.cc/files/avrdude-5.4-arduino-0010-src.tgz