If the installer told you that "you couldn't use the Kenwood's crossover and sub controls until you got rid of the factory amps"' It sounds like it has something to do with the wiring. Sounds like you will have no problem, as soon as you replace the amps. Just my opinion.
I also replaced my factory speakers with pioneer brand, and was very pleased with the sound. Good luck with your project.
Let us know when your situation is resolved.
Thank you, I plan on doing the sub/amp swap as soon as I can save up some $$$. I actually now have to get the back bumper painted because I caught some kids leaning all over it and one left butt scrapes all over. Luckily I only have a $50 comprehensive deductible and my insurance already cut me a check. The body shop that I go to gave me an estimate of $600 to do the back bumper so that low deductible is definitely saving me money. I swear I'm going to start carrying road cones and caution tape to put around my car when I go anywhere. It's not enough that I park as far away from everybody as I can.