[need advice.]

I have around that power as well and my factory electrical handles it ok at 65AH bat and 140amp alt. I would like to see how that yellow top handles the power. hook a volt meter to it with the car on and film the readings.

[new at sound quality]

If you think it sounds good than it really does not matter how much the speakers cost. About 80 percent of aftermarket speakers with an amp is going to sound better than pretty much every factory system. If you do reasearch you can get some fairly priced speakers and an EQ and it will sound good with all types of music

[Bass Knobs and Equalizers, Clarion EQS746]

I think you should hook your clarion eq up to the soundstream amp and ditch the bass knob. Then turn the sub level to the max and tune the amp with a -10db 40hz tone. This way your bass will be 10db's louder than the bass in the song when you turn the level up. If you want more flexibility just use a louder tone when tuning like a -5db.

Or you could just set the bass control on the headunit to normal, turn the bass knob to the max, and then tune it with a 0db tone. then turn the bass control on the headunit to max and leave it there and use the bass knob to control the sub volume.

Either way will make your bass loud. Personally I use the second way but that is because i do not have an equalizer like you do.

[Subwoofer SQ question]

Yeah i'd say its the box man. Prefab boxes are known to be tuned incorrectly. Look up some youtube vids of boxes that people built themselves to get an idea of the process and result.