1999 Lincoln Continental OEM Alpine

Hello.
I replaced the Alpine OEM with an Alpine ILX-W650 double din. I hooked up the door speakers and subwoofers (2 oem 6 x 9 subs are in the deck corners controlled by an oem amp) to the new head unit. The system sounds ok and the subs sound strong. I have the subs hooked up to the sub output on the head unit, and although the headunit cannot control the output, crossover or anything pertaining to the subs, it still does get a signal to turn on and offer nice bass. The oem amp seems to be overriding everything from the head unit. Opening the subwoofer controls on the head unit (off, on, crossover, etc...) does not do anything, as I cannot shut the speakers off, adjust them, or anything. Basically just enjoy the bass that the amp gives and stop complaining type of deal. Here is the issue. The door speakers sound fair at best, so I installed a new set of front and rear (6.5 front door, and 6 x 8 rear door) Infinity Kappa speakers. The sound from the doors is decent on the highs and ok on the mids, but NO bass is coming through them, NONE. The entire system, AT THIS TIME, are hooked up to the new Alpine head unit. I decided to disconnect the rear amp for testing purposes, by unplugging both the input and the output plugs. Now the Door speakers ROCK, and I mean ROCK. Bass comes through hard and sharp. The rears are a little muffled on the highs, but really kick on the bass. The fronts have just a little less bass, but are incredible with the highs so we have some balance. I really don't want to completely abandon the subs in the rear corners if possible since they have their own amp, but I'm not sure how the amp is messing with the door speakers. I have a Fosgate 400-4 4 channel amp that I could hook up to the doors and just run the wires from the amp to the speakers and abandon the factory speaker wires to the doors, but I hate to do all that work powering the amp through RCA's for signal, only to have the same problem. If I go through running #4 to the battery and running wires etc... and the rear amp just shuts down the Fosgate, this would only mean I am just powering the door speakers better and abandoning the factory amp and subs. They sound pretty good right now without the amp. I want it ALL. The only reason I am really wanting to keep the 6 x 9 subs is that they really do sound pretty good. I only want the factory amp to run the subs, but not to interfere with the doors. Does anyone have any insight into this??
TIA

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1999 C5 Corvette
1999 Lincoln Continental
2001 Jeep Grand Cherokee

sounds like you didn't hook up the parking brake wire properly, probably "just grounded it". alpines don't work that way, they have to see the parking brake engaged 2 times for it to work. The controls are probably all greyed out?

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33 years as a installer now just a retired old guy. Favorite thing to install/topic are remote starts/car alarms. Stop using test lights!!!

Nope. I do have the parking brake hooked up properly. All functions work perfectly and are NOT greyed out. The subwoofer amp has everything built into it so it doesn't allow anything to interfere.
Every other function works perfectly, including bass, treble, EQ, etc...

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1999 C5 Corvette
1999 Lincoln Continental
2001 Jeep Grand Cherokee

you should be able to, the deck doesn't know you have a amp hooked up to it. Really odd, I've done probably 50 of those deck and never had problem with turning the sub on\off and controlling the sub up/down. id try doing a factory reset on the deck. gotta be something in the menu that switched off.

checked our floor model and sub button on/off all working

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33 years as a installer now just a retired old guy. Favorite thing to install/topic are remote starts/car alarms. Stop using test lights!!!

I've installed dozens of car stereos in my 59 years. I worked for Circuit City's road shop when I was young. I have 4 Fosgate amps in my Vette, and 2 amps in my Jeep. I believe this Lincoln has something that is in the factory wiring, that either goes to some type of processor or has something where it inputs. What I may do since I have installed the speakers and disconnected the factory amp, allowing the speakers to really thrive as they should, is skip the 4 channel Fosgate amp and just allow the radio to power the speakers and completely remove the factory amp and install a smaller Fosgate P200-2 bridgeable amp, and utilize the on board bridging ability on the amp to control the 2 subs, or I can use the head unit's subwoofer crossover ability to control the amp. The 2 6 x 9 subwoofers, while 22 years old, have really NEVER been used, as I received this low mileage car from my 85 year old mother (Original owner) and she said she can't remember playing the radio once, and the car was always garaged. Guess we'll find out. Right now the stereo, without the rear subs, sounds REALLY good (I listen to 70's ROCK). I just would like to hear how the subs sound when the doors sound normal.

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1999 C5 Corvette
1999 Lincoln Continental
2001 Jeep Grand Cherokee