Another way to look at it... Build your portion of your ship (command module if you will) you expect to be in orbit with. Turn on Center of Mass and place the RCS right in the center. Then build the rest of the ship that you'll use to launch into space. Or build your entire rocket, take off the parts you'll use to launch the command module, turn on CoM, align RCS in the center of CoM, then reattach the rest of the ship.