reaper911, I'd recommend reading
http://www.bcae1.com
that site answers a lot of your questions very concisely.
the "gain" setting on your amp (actually it's properly called "input sensitivity" since it's not truly a gain adjustment) is not used to vary how much power the amp puts out or meant to act as a volume knob. The only purpose of input sentivity is to match the input stage of the amplifier to the RCA line voltage coming from the head unit (usually between about 2 and 5 volts depending on the head unit.) I've explained this so many times now, but once again if the gain is set too high, thr amp's input stage will be over-sensitive and you'll overdrive the amp. the amp puts out no more power, but it distorts and clips, causing DC voltage to go to the speakers and that fries speakers, as you found out the hard way.
If your head unit is a 4 volt unit then set the amp gain to "4"
If the system isn't loud enough then adjust the bass level at the head unit, or buy a larger amplifier or better subs or both.
set the LPF on your amplifier to 60 to 80Hz.. for 12" or larger subs I usually don't go higher than 60Hz if you want tight bass.
as for power output, your amp only puts out 900 watts at 2 ohms at full volume with a test tone. actual power output to a reactive load like a speaker playing music at normal volumes is several magnitudes less tahn 900 watts. This has to do with power and sound pressure relationships.
as for fusing.. 30A+30A is 60A of current. that * 14.4VDC at 80% efficiency for a class D amplifier is about 690 watts RMS at best. I'm guessing either your amp has a third 30A fuse, you have the wrong fuses in the amp, or your 900 watts is "pwak" and not RMS.. since peak is generally two to three times the real power output.
This would also explain why the subs sound weak with the gain properly set. your kenwood amp is just too small. you need to get a better amplifier that puts out a real 900 watts RMS at 2 ohms.
Then the subs will hit properly, and you won't blow the coils up with clipping by overcompensating with gain for lack of real power.
ya know with those two subs.. an Orion275HCCA would be a great amp at 1 ohm stereo. You'd get 300wRMS per sub, and it's be true, balls to the wall class AB amp power. Plus your amp would be "rated" in competition as a 2x75 watt amp (at 4 ohms)
you can find 275HCCAs on ebay pretty often in good shape for a good price