I am not very audio technical so please bear with me. I have read the AVIC-D3 installation manual and I have searched this forum for an answer to my question but as yet have found none.

I have the D3 hooked up to my car speakers-2 in the front doors and 2 in the rear doors. Although I did not do the installation myself I understand that because I am only using the HU power these speakers must be connected using the speaker wires coming out of the power cord cluster and not the RCA outputs.

The first step in upgrading my speakers is to add a powered subwoofer. Page 9 of the installation manual shows replacing the rear speakers with a sub using the speaker wires from the power cord. I want to keep rear speakers so this is out. Can I keep my door speakers wired as they are and add a powered sub using the RCA output for the sub only? It’s not an all or nothing hook-up is it? And how will this effect the voice command feature? Because it is only sent to the front speakers will the sub mute?

Leave all the speakers wired up as they are, hooked up to the D3's amplifier. Just run an RCA cable from the D3's subwoofer RCA pre-outs to the sub amplifier and you are good to go.

Yup, exactly what HiFiSi said... Just to clarify, you would run the speaker wire from the subs directly to the amp you install. So no wires really go to the d3 besides the RCA's and the remote turn on wire which are both run from the amp.