I used my sub to go to multiple spots on the level, and I could never find a way inside the actual location. Is there a way inside of the locations or is that not possible? I am travelling to bases and cities not alien locations. I can see the outline of them sometimes but can't actually find a way in. Any help is appreciated.

So... What is the location you are trying to enter? Is it a ruin? City? Something ells? For ruin you just melt the wall with blow torch. And City you press "C" or your key for the command menue and then klick "Enter (Name of City)"

An "Enter Location" button should appear as soon as you get near enough of the location waypoint. You can't physically see or interact with an actual base, you are just notified you arrived and then get a menu with tabs for crew recruitment, store and map for next travel/mission selection.