It depends how your gains are set in the first place. Clipping is the least of your worries and a bit of clipping on the input side can't hurt your stuff very easily nor will it be very audible. Clipping heavily on the input side however sounds like **** and if ran hard, then it will hurt your stuff. Clipping on the output side ONLY happens at high volume on the output side, and may or may not hurt your things, depending how clipped you are..
3rd time in 3 days I've had to post this, I about want to make a thread.. MINOR CLIPPING HURTS NOTHING! In fact you WANT to clip your stuff, if you want any output out of it. Most music, even rap has a 3-6db crest factor, rock can be as much as 12, really well recorded stuff, 20db or more crest factor. Crest factor is the difference between a sources max volume and it's average volume, when it's recorded. So even heavy rap is 6db quieter on the average than it is at big bass lines.. So if your amp NEVER clips, so just under clipping on the big points, it's putting out -6db worth of output on average, or 1/4 the power.. Your 1200 watt amp on "average" is only producing 400 watts.. That's why it's quiet. Minor clipping is mostly inaudible as the distortion it produces will be filtered out by the subwoofers natural inductance. Not only that, the coil can doens't see that much more power, since the higher order stuff is filtered. 3-6db of clipping wont' sound bad when it clips, won't break the sub and will make your sub produce around 2x the average power ,so you'll be getting 800ish watts on average, with peaks at 1200 clipping slightly and lesser peaks just being maxed out as normal..
If you don't have a tone, just use music. Turn your gains all the way down on everything. Put HU at 3/4 volume, sub level all the way up, in most cd player it's just another preamp gain that rarely clips... Play a song in the low 30's, white girl is a easy one most people have. Turn the gain up on the amp until the sub stops moving futher or sounds distorted. Once that happens back the gain down a bit.. Your not going to be clipping all to hell at that point and it should get loud.. The SMD is what's messing you up, just set the gain by ear and use common sense. When the gain knob stops producing more output STOP. Remember how loud that is and you'll know the limit of your equipment.
A -3 or -6db tone can do the same thing. Depends how much gain overlap you want, personally if I use tones it at least a -6 and I just watch my volume knob, loud tracks turn down a hair, quiet tracks I have plenty of room to turn it up.