ISBoxer has a UI Mod component that allows you to write macro's outside game and import them into the game. You can also bind keys to these macros which for the most p art will override your default keybindings without altering the defaults.

So you can have keybindings for your main character for solo play, and a seperate set for multiboxing, without having to worry about conflict.

And yes, you can do a complete setup without ever setting foot in WoW, then load... however I find it's easier to debug smaller steps so I build my setups a few features at a time.