yes, getting lined up with the runway on the simulator is more difficult than it is in real life. but it is still excellent practice and has helped my landings significantly. On the sim, try your best to get it lined up, but dont worry too much if you are just to one side or the other. Practicing the glide slop, controlling the plane while its coming at you at a lower speed all while finding the right amount of power is key to getting good landings.

Jeremy