So after starting this thread and getting all the great advice, I was able to get a better handle on the base management stuff. Expanded to global coverage, ramped up my manufacturing, shifted gals around to have some experienced ones at each base in case of a crackdown, worked out a standard base defense loadout, actually got it all manufactured and shipped out.
Then after I don't know how many in-game months, I finally got a crackdown. And they wiped the base out. LOL. In my defense, it was the newest of my bases, really just a radar outpost type base. I hadn't transferred anyone good there, it was just new hands stuck in a dojo and half-trained at that. Plus it was a stargod crackdown. At the point I'm at, only my A team could have repelled this attack. I actually did better than I thought I would, but there were a bunch of cyclops and most of my weapons just tickled them. In the end all I really lost was a few mil and some time.
I did notice one thing I was curious about. The base in question was in antarctica, and when they were searching for it I had a ship spawn in Africa, with the crackdown flag, and it literally flew slowly over my African base as it was headed south. I thought it was actually going to attack the African base and held my breath waiting for the base defense screen, but it just kept moseying south.
When they're searching for a base, do they wait until they're in the actual area or is it scanning from spawn point to despawn point?