the BEST way to set it up is to get a 50hz frequency, along with other frequencies, (at 0dB)
play them at 75% headunit volume with no bass enhancements at all,
set everything on the amp to zero,
wire an oscilloscope to the output terminals on the amp,
set the scope to the correct input impedence,
slowly increase the gain on the amp until the sine wave clips,
(goes flat at the top)
reduce the gain a touch for safe measure, then make sure it does no clip on any of the frequencies, if not, then take the scope off and connect the sub.
but make sure the sub is suited to the amp.
thats how to PROPERLY set up a sub.
it is very hard to hear a clipped signal in bass waves, so be careful setting it up by hand, clip signals kill subs!
however most people never bother with that, thats only for very expensive systems.
however if you have access to an oscilloscope there's nothing stopping you!