Which keys do you want to remap? Remapping the standard keys will affect both keyboards (I think). But if you are talking about some flashy extra keys on the logitech, this is easy.
It's different for console and X.
For the console, the keymaps are under /usr/share/kbd/keymaps/i386/* (on Slackware anyway). These are loaded with the loadkeys command. You can copy one of these and modify it to your requirements (I put mine in /etc/defkeymap.map) and load it at boot time. (You can also compile it into the kernel).
For X, create ~/.Xmodmap and put 'xmodmap ~/.Xmodmap' in your ~/.xinitrc (or ~/.xsession). See the xmodmap man page for the syntax of this file. Use xev to see the keycodes for the keys and plug them into your .Xmodmap.
If you're talking about remapping the whole keyboard, I don't know if this is possible yet (no way to differentiate between keyboards -- I seem to recall reading that this is being worked on, but I can't remember any details).