Just a quick question about actually starting the emulator.
Ok. I have downloaded the pj64x n64 emulator and some n64 games. I have ftp'ed my xbox and have put the games in the games folder and adjusted my evox.ini file accordingly(do i even need 2 do this?). When i put the emulator in my apps folder i realised that it does not have an executable (default.xbe) file. Maybe this is a very basic question but what file is actually used to start the emulator/command line for evox. If i am going about this totally the wrong way please direct me to a relevant tutorial, etc.

It should have a default.xbe file. Try unzipping it again to check if it got lost. If that dosnt work download it again.

You could try downloading a package that has the binary in it and not the uncompiled source.