If you overdrive the amp, you will cook subs plain and simple. Depending on the level of the RCA inputs and the sensitivity range of the amp, half way on the gain could very well too high. The gain setting is not a "power level" control. It is intended to match the input sensitivity of the amp to the voltage level of the input signal. Nothing more. Too many people just don't understand that. Another thing that many don't understand is that running the head unit at high volume will cause its outputs to clip. Send that downstream to the amp and now it is amplifying a clipped signal. Clipping is clipping; it doesn't matter what the culprit piece of equipment is. Adding bass boost will cause it to clip sooner.
Also, there are two ways to "blow" a sub. You can exceed its thermal power handling and you can exceed its displacement limited power handling. The first is a factor of how well the motor structure sheds heat. This is what the typical power rating is referring to. It is mostly independent of enclosure size and type. The second is entirely determined by enclosure size and type. The sub needs the enclosure to keep from exceeding its excursion limits at higher power levels. Smaller sealed enclosures typically provide better control of the cone at higher power than a larger sealed box because the change in internal pressure in the box is higher when the airspace is smaller. Vented enclosures provide excellent cone control at or above the tuning frequency; however, they provide almost no cone control below the tuning freq and it is easy to damage the woofer with frequencies below the tuning frequency of the enclosure. For this reason JL as well as many other manufacturers recommend a subsonic filter be used to keep frequencies below the tuning freq away from the sub. It sounds like this is what you did to the first set of 12W6's. You exceeded their displacement limited power handling.
