I honestly can't say the difference will be huge, BUT... if your head unit has special RCA outputs specifically for subs (as many do) then it would be good to run some RCA's, that way you can use the built in levels on the head unit. On mine, I have the subwoofer levels all the way up with the overall bass setting at 0. That way it takes some bass of the full ranges in the car and sends most back to the subs. I can push the overall system harder without the full ranges in the car distorting badly and sounding like crap.
EDIT: almost forgot to ask, but I have a buddy that want's some boom in his trunk and I told him I'd hook it up for him, if you are able to, could you snap a picture of what you did behind the radio to run the high levels? I'm curious as to how to set those up. I'm assuming you dont actually disconnect from or back. I'm guessing you just splice into the front or back ones and split the signal and send it to the amp correct?