Problem replacing 6X9s in a car w/ Bose

So I get some nice Kenwood 6X9's hooked up in my boy's 1993 Infiniti Q45 and when I turn the music on they sound like crap.  Not only do they sound like crap, but they aren't as loud as the stock 6X9's and they make an interference/humming noise when the amp is hooked up.  I'll try to explain how the system is set up. 

 [b]With all stock speakers:[/b]
He had a shop install an amp and subs.  They used an rca converter which is tapped into the rear 6X9's.  The stock 6X9's seem to be powered cuz they have an attachment to the magnets that look like little amps.  They have a harness with 4 wires that plugs them into the car.  Two of the wires are audio and I am guessing the other two are power and ground.  It looks like the shop remoted the amp off of one of the 6X9's power wire.  The bass sounds good but now he needs new interior speakers.

 [b]When the Kenwood 6X9's are in:[/b]
So I unplugged and removed stock 6X9's and put the Kenwoods in.  I tapped them into the speaker wires of the harnesses that plugged into the 6X9's which I'm sure is coming from the factory amp.  Remember, this harness has the power and ground as well as the two speaker wires.  Theses same speaker wires are what the RCA converter is tapping into which is giving the signal to the subs.  Why are the subs sounding right and not the Kenwoods?  I am using the same signal for the speakers but the speakers sound like pure ass and they are low as hell.  Yes I have the polarities correct, plus I tried them both ways and it sounded exactly the same.  And why are the subs playing a humming interference noise when I hook up the Kenwoods?

So will he have to get a new HU and do a full bypass to be able to add new speakers?

You're right about the speakers-those are amps on them.  The thing about Bose is they operate at a lower resistance (usually 1 or 2 ohms), and the amps are set up to push them.  So when you hook up a 4 ohm speaker, they will play at lower volume and have slight distortion.  Usually when something goes bad in a bose equipped car, you end up changing the whole system and running new wires. 

The humming you hear is probably a ground loop going throught stock amps and getting transfered to the sub amp and the to the sub itself.  You can probably stop it (i think) by grounding the sub amp at the negative side of the battery but the won't solve the speaker problem.  Easiset thing to do is get an aftermarket head unit/speakers and run new wires. 

Hope that helps