Instructions for customizing controls is in the second post. If ya can't work it out install v1.5 of mupen64plus for Linux, use the GUI in that to define the keys and then copy over.

i may know the issue for saving. i don't believe I enabled controller memory paks by default. Only the innternal memory found in the cartidge (much smaller).

Quick fix if its still not working:
leafpad /home/user/.mupen64plus/blight_input.conf

You'll see on about the third line plugin=1, change this to plugin=2 which will enable the controller pak memory.