A set of Regions (any and all regions you have active at the time) is saved per Character Set. Saving as Auto on one will not affect the other Character Sets at all.

Saving as anything other than Auto means it wont auto-load, and you can manually load the set through the in-game control panel (via the drop-down above the save box) or via a Repeater Regions Action. I use 2 different region sets, one for healing 5 man and one for healing up to 40-man (e.g. battlegrounds).