you should be able to set multiple 'accounts' up on g-authenticater.  There is an option in the app to do so.  I've created a couple one accidentally for the same account on eclipse pool but luckly only matched one.  I then deleted the one I did need to use.  You should be ok as long as you tie in the correct codes when you sign up.  

I have no experience with setting up on MtGox but it should be the same as g-authenticater is developed by google.