as far as i know that assumption is correct, if you have them into the usb or ps/2, the kernel doesn't know the difference.
in terms of hotkeys, that depends on your window manager. you need to be able to map specific F-keys to specific commands in order to use the hotkeys. the first thing you do is use xmodmap to change the keycodes to some F-key, then use the window manager to map the F-key to a specific command.
for example, i set the keycodes for my logitech iTouch buttons to F21 and F22, then i used icewm's key options to map F21="aumix -w -2" and F22="aumix -w +2"
the xmodmap is the tuff part. you need to use xev to figure out what the keycodes are for those buttons, then xmodmap is something like this in .xinitrc :
that's about it, i hope i made sense