Kris, i might be able to help you with that - you can do a lot with a bit of registry tweaks and batch files (on windows) - also i think i posted something about this here, long time ago (though it has evolved a lot since).
in any case, i do run different sketchup setups (plugins etc.) with only one installation - say one geared towards modelling and the other rendering. i was thinking of some video tutorials to come in the near future and i could be showing the steps for this too - my whole setup is a bit complex and my time is not super friendly with me right now, but i'll get round to it.
the only problem is that if the toolbar get messed up - you still have to restart SU to get them back.
(but getting them back is then pretty quick).