The X53 (like any other joystick !) is quite usable in shipsim.
If you want, you can try a setup similar to the one I use (mine is a X45 but it must be quite the same!):
http://www.shipsim.com/ShipSimForum/index.php/topic,2202.0.html
About how to set it up ... Just use the "controls" menu and you should not have any problem, the UI is quite intuitive .... !