Let me see if I can help a bit; So the story so far ;

Speaker ; Front Component L+R, Rear 6x9 L+R and Subwoofer.. want to able to control all.
HU ; Stock that support Front L+R and Rear L+R, no support for Subwoofer and No RCA.
Amp ; 4 channel... think now connect to Subwoofer from HU Rear and HU Front connect to Speaker (believe both Component & 6x9)
Fader Function - Rear Subwoofer only, Front all 4 speaker.... (Correct me if wrong)

Alternative ;

1) Change HU that can control everything saparate and with RCA... Saparate for Front, Rear and Subwoofer... something like this... Connect Front RCA to 4chAmp to Speaker, Subwoofer RCA to 4chAmp to Subwoofer and Rear 6x9 connect to HU direct powering.



2) Get another 2 channel Amp. Stock HU Front to 4 ChAmp to Component, Stock HU Rear to 4chAmp to 6x9 and Split the Stock HU Front (With Splitter) to 2chAmp to Subwoofer. As the Stock HU no RCA, then need to get HiLo Converter that can work with Splitter.

3) Get a processor... everything go through the Processor. This way not cheap as maybe need active crossover.. hahaha...

By the way, what happened to the 6x9? Went into the Tong Sampah?