So I just got this game and I'm playing the campaign mode. I try to build my base, but once I got my base all built underground, it wont let me deploy my brain deep inside! It claims its blocked by the terrain even though I've built over it. What stupid thing am I doing wrong?

Use the "infantry brain" or "installation brain" options underneath the deployments tab.

See, the bunker you build in Campaign is a "blueprint" which will be laid down after you assign the funds to it from the world map, the deployments are part of that blueprint telling the game where to place soldiers and brains.