As for room size:
Barracks, Training Room need to be large. Power room takes up almost a third of my base so leave space for that. Barracks have a few bunk beds (watch your minions usage of them to see how many) and shedloads of lockers which bumps up your population limit - I think its limited to 100 tho.
Freezer doesn't have to be too big - I have three or four racks and that's enough.
Armory - make sure you keep the guns away from the entrance as they generate heat.
Generally have one entrance as it's easier to tag and capture/kill enemy agents when you see them coming in. Put all the "non heat generating rooms" (barracks, staff room, mess hall) nearer the entrance than the others. Put a strong room a little further into the base so your minions don't have far to run to fetch a briefcase to carry materials into your base, but keep an eye on it. Have a big enough armoury for about four cells and two interrogation chairs - you can have two armouries or more, one with non heat stuff like control panel and one with all the guns and perhaps one with the cells/interrogation stuff.
Inner sanctum doesn't need to be huge, big enough for the impressive desk and chair and perhaps a few stolen vases and stuff that you collect
Control room needs to have enough for about eight control panels I think to do everything, plus quite a few databanks (I don't really know the optimal size here).
Infirmaries don't have to be large as they're just a pill dispensing stand from what I can tell.