It's not hard to roast most woofers with 1200 watts. You are simply exceeding the thermal limits of those woofers. You might want to consider a stronger sub if you're smoking your subs to get the sound you want. I'd say a larger sub as well, but if you have a box built for a 12, find a 12 that'll handle 1200-1500W continuous that'll play well in your box.
Dunno what your other sub is supposed to handle, but the Q is only rated at 1000W. It's like if you have a sports car and run the engine red-line constantly and wonder why you blew the engine. Run it up to max here and there and you're fine, do it for 10-20 minutes and you're likely to have some problems.
Gain up or down has nothing to do with nothing, if the sub is smoking you are driving the sub past it's limits period.