If it's just the sub you are running from an amp, the only options I'd imagine you have for setting it up is the gain (kinda like a volume) but used to match the signal output & get the level to match that of the 6x9's. Maybe some crossovers which you can use your ears best to get the sub working & sounding where the 6x9's begin to struggle.
Still test the phasing of the 6x9's though.
Some dynamat behind the quarter panels in the boot will do wonders to the sound & how loud you can turn it all up before distorting.