KitsandKids, we don’t know exactly how many commanders there are but it’s a lot. Apologies in advance for this explanation as I’ve got some bits from the book and some from the show and it gets more difficult to remember what’s from where but I’ll try.
In the beginning there was a crazy, right wing religious group, The Sons of Jacob. The Waterfords, Cmdr Pryce, probably Cushing (as we saw he was quite high up and Serena mentioned him being an old friend of theirs) as well as many others were at the forefront of the movement. It had factions all over the US and we’re seeing just one district (in what was Boston). Anyway, after recruiting more and more people (ones like Nick who were not religious zealots but disillusioned and not really clued up as to what they were getting into) all the factions came together and overthrew the Government, Congress & the Supreme Court leadingng to a war and the proper inception of Gilead as we see now.
I think DC is still the capital (Fred mentions frequent business trips there in S1) but basically we’re only seeing one state and it’s structure/hierarchy. We’re led to believe this in mirrored in most states though, Alaska & Hawaii being the exceptions. Possibly a few others are still more war-torn and unsettled (Florida- the war was going well though).
I think that the reason for so many Commanders ruling one relatively small area is because you need some power of number to rule such a totalitarian regime. It projects ultimate power, strength and an iron fist rule to the little people and keeps them fearful and rule abiding.