it is all down to key bindings.

you either have totally separate bingings on each instance or you have some common and then individual bindings.

Xzin's write up goes into this, he uses X-keys Pro to set individual keys for spells on separate characters.

with a simple keyboard you could use 1-0 for synchronous spells

then Shift 1-0 for char 1 spells
and CTRL 1-0 for char 2 spells

even with the built-in key bindings system this is possible.

a useful addon called bindpad allows you to map key bindings directly to macros, but unfortunately only allows one binding per macro.

Bongo Bars, if I remember correctly, will allow you to map multiple keys to each bongo bars button.