01 03 ford amplified systems?

ok so i hope im not the only one to find these systems confusing..... what i'm trying to do is install an aftermarket deck in a car that calls for the amp integration harness eg. Best Kits' BHA-5700 or Scosche's Fdk9....... if you have ever worked with these then you know they can be quite confusing.... im just wondering how exactly are you supposed to wire the harness, i mean im not a complete n00b but between the 3 harnesses, 3 amp ground wires, 2 remote turn on leads and 2 sets of front speaker leads i'm just looking for some certainty as to how to wire it up properly when i have used them before what i do is take the remote from the new head unit and the 2 from the harness and splice them all together then the left front's all together the same way and the right fronts all together the same also then that leaves the 3 amp grounds on the harness which i leave alone and dont use.... so far each time i've used one of these(once on a 03 mustang with the mach system, and once on an expedition that had a factory sub) all of the speakers work but the bass is overwhelming please help me out any way you can, im just an installer who's striving to do things right.....thanks for your help

ok the harness i use has 3 plugs, one only has 2 wires on it which i believe is for mute on the factory radios.... that leaves the 2 harnesses, ones the harness that has power, ground, acc, and what not and the 4 sets of speakers, the second, which is the smaller of the three, has the 2 remotes(blue/white) 2 amp grounds (BLACK/ white) a white, a WHITE/ black, a grey, and a grey black, those are the other leads im referring to, check out the pic of the best kits one cuz thats the exact one i'm using, the metra site doesn't show a pic of the amp int. one