Typically, I put about three levels in a base; if you try to make more, you'll have less than 10 feet of clearance (the COT door works well for measuring this) and will start to run into clearance issues, even when your character isn't that high (the computer apparently has to allow for the possibility your character needs that much clearance). The cement walls, without most of the wooden paneling (just leave the same amount at the bottom as the top) works well as a measure of one level, and leaves room for a ceiling.
For floors, well, some people use the docks in Landscape to do floors and ceilings simultaneously. I find the big docks to be a bit thick for my liking; besides, I like light ceilings. I might use the dock to set the floor level until I have the surface covered in what I want the surface to be, though; although, usually, I'll just slide a piece of office flooring around (Ctrl is so helpful here, because then I know it's always at the same level no matter where I move it). If I use pieces for the ceiling, I tend to use the larger shower floor, in bathrooms, the underside of that is solid with no drain. They lay perfectly next to each other if you set your grid on 1/4.
You can build either above or below the base, too; you can move the base entry so that that's where you enter, if you wish, or you can access it with internal base porters. The base plot goes WAY up and down; the only thing to keep in mind is that you cannot build to the side of the rooms on the plot, you can only build up or down from whatever rooms you have. If you want to build higher (or lower) than the base itself, then you'll have to move something like a piece of flooring up or down to build on.
My best advice is learn all of the commands in editing the base, it will make life so much easier! :)
-Dacy