Whilst the station is small, moving it around will be rather easy and safe, but as it get's larger, it will take more and more thrust to get the same effect. You also run the risk of ripping your station apart, so I would strongly advise you get everything into it's final position as you build it. Symmetry is not a huge concern for a station, as you will not be 'driving' it around. If you have a normal ship, then yes, the engine must be thrusting through the CoM else it will spin the ship.