Does anyone know if I can put an indash (stock) CD-player and have it still control my 12 changer (stock) in the trunk

I'm not sure, but I'd be willing to bet money that the OEM in dash CD player does NOT have the controls to operate the CD changer. I think you have to pick your poison or go aftermarket.

I'll also give you a warning if you have the BOSE premium sound system like I do:

I don't have a changer in the trunk so I got a CD/MP3 indash player and some subs in the trunk.

In order to run the signal to the amp and subs I had to bypass the factory amp. It is a big pain and I ended up taking it to a stereo shop and have them do it.

If you don't have the premium sound system the in dash CD player will work.

Crutchfield sells a device that goes inline between the aftermarket stereo and the aftermarket wire harness. It gives the amp the signal that it needs to make the speakers operate properly, without having to re-wire the rears.I bought it so I could install my unit. The thing that I found out was, that with the BOSE system, the only wires in the factory harness that will match the aftermarket harness, is the power wires. The speaker wires in the factory harness do not match the speaker wires in the after market harness. Four different "wiring digarams" were given, with the warning "If your wires do not match the sample diagrams given below, you must contact the dealer to obtain the right wiring diagram for your car". My wiring did not match any of the four samples given, and I was not going to go to the dealer. So...I sold my JVC head unit and sub on ebay today. The bright side is that I get to keep my stering wheel controls and my radio information in the HUD

Thats a shame Austin.

I ended up just paying for a stereo place to do the install. They used a part similar to what you talked about on Crutchfield becuase I'm sure they didn't rewire my rear speakers.

My stereo sounds AWESOME now I just lack the steering wheel controls. I can always fix that with a $60 part but it wasn't that important to me right now.

Thanks guys. I've been off for a while. Just moved to Charlotte. I ended up putting the OEM tape deck to keep the changer. I also just installed 2 10 inch with an amp. I just used a Line oput inverter(ran off the 6x9s)
It sounds great. Anyway, thanks again.
Nick

Sounds like it worked out for you. I ran into the problem of having to run them from the 6x9s. The car stereo place sold me a part that allows me to run it straight from the deck instead and I got much better sound quality and much louder jams.