That's the way I do it :
One main hotbar (#1), one extended hotbar (#7)
One additionnal hotbar (#2) for skills that I don't have to use really quick during combat (Like Protect).

When I use the toggle button, it only switch on 1 and 2.

And for jobs that have mutually exclusive skills, I make a macro to place the right skill on the right slot.
For example, in my Defiance macro, I'll assign Inner Beast and Steel Cyclone to two slots, and on my Deliverance macro, I assign Fell Cleave and Decimation to the same slots.

Same for SCH and SMN with the pet skills on the extended hotbar.