The ball goes into the socket head, the socket head goes into the hole in the ship, your choice of short or long stem goes into the ball, and the base goes on the other end of the stem.
If you just want the ship to stand perfectly level, that's about it. If you want to use the pivot head to put the ship into a banking pose while on display (or to put it at an angle in classic ST:TOS style when it's dead in space), you may need to sand the ball down a little - personal experience with these stands under B5:ACTA ships is that the ball is a very tight fit and won't move unless it has been sanded first. But if you overdo it, the ship will never sit level. This is less of a problem with smaller, lighter ships, so if your Heavy Cruiser won't stand straight, use a pin or something similar to extract the ball and put it into the socket under something like a Frigate instead.