1. Well, it depends! Looking through the list will give a selection of Council/5th Column underground style bases, which you will probably have to select and have a walk around to get a feel for them to see if they suit you. I usually do that. Load in a map, set it to "Empty" part way down the Villain list, give it a single collectable and some filler text so the AE doesn't bork at you, then just walk around and get the vibe. Also, paying attention to the layout of Xs and Os and so on on the mini map.
However, if you want a shinier sort of underground base then having a look at the Praetorian Tech or Bio Labs is a good go to, so have a look at those.
2. Well, we don't have the option in AE of a locked door, so the best you can do is defeat a boss and have his clue say something about a keycard and trigger a glowie/whatever further inside the base. A lot of AE building is trial and error, so checking out one of the guides here or checking out how other people have done them is going to help. Other than that, happy mission making!