I'm never quite sure what squares I'm suppose to control, especially in positions that aren't official openings or unconventional openings?
The best way to know what needs to be done is to grasp how the pawn structure in the center affects the course of the game. Read "The Art of The Middle Game" by Alexander Kotov and Paul Keres. Kotov's chapter explaining the five possible pawn centers and how to proceed is the finest source ever written on this topic.
Those possible centers are: open, closed, fixed, mobile, and dynamic.
An open center is where only one or no K or Q pawns are still on the board. Fast attacks on the K and Q files are required and immediate castling for safety.
A closed center is where pawns lock in mutual pawn chains such that neither side can advance a central pawn. Wing attacks become necessary and castling can be delayed.
A fixed center is where the two K pawns face each other so neither can advance and the Q pawns are off the board. Or, the Q pawns exist in the same manner and the K pawns are gone. Play will result where each side tries to place a piece(usually a Knight) on the strong point protected by the central pawn such that the piece cannot be attacked by an enemy pawn advance. This is called an advanced outpost and when it occurs, victory for that player is likely.
A mobile center is when one side has both central pawns and the opponent has none. The constant threat of these pawns advancing keeps the enemy too busy defending and lacking time to mount a counter-attack.
A dynamic center exists when the other four possibilities have not yet been decided. You should try to play for the type of center that will be stronger for your side.
Finally, look at your central pawns. If the K pawn is further advanced, look to attack on that side or in the center. When the Q pawn is further out, attack on the queen side. Kotov can provide much more detail. Read the book!
Usually you try to control squares to prevent your opponent from putting a piece or a pawn there. Or, the other way round, because you want to put a piece or a pawn there.
To me that is the way to think about this problem. "Controlling squares" is a very abstract concept. "I really don't want his knight to come to c4, so I play b3.", that's a very concrete idea.
Often this means controlling central squares, because if your opponent puts pawns there, he will get a strong centre. Or you control the square in front of an backward pawn, to avoid it being pushed and exchanged. And of course you try to control the squares close to your king, otherwise you'll fall under an attack.
Try to find out which moves of your opponent you want to prevent. Don't worry about controlling squares.