Hi All. I'm new here and this is my first post. Just got my E on New Year's Eve.
I wanted to install my JVC head unit (KD SH-707) using it's own amp and bypassing the factory amp on the E. Also run an MTX 6500D amp to 2 Kicker Comp VR 10's. Searched the boards and couldn't find the wiring diagram for the E's amp anywhere, so I hope I'm not rehashing old news here.
I wanted to use the factory wiring without having to run new wires to all the speakers. I got the wiring diagram from my local Honda dealer. After unplugging both plugs from the amp, I hooked the powered speaker outputs to the factory output wires of the amp. Worked great and was really easy to do. Here's the wiring color codes if anyone's interested.

Pin A6 Front/Left + Grn/Blk
Pin A13 Front/Left - Grn
Pin A7 Front/Right + Grn/Yel
Pin A14 Front/Right - Blu/Yel

Pin A4 Rear/Left + Blu/Wht
Pin A3 Rear/Left - Blu/Blk
Pin A5 Rear/Right + Pnk
Pin A12 Rear/Right - Blu/Yel

These wires are on the big plug on the amp.
Also, the tweeters are connected to the front outputs.

Very helpful, Thanks! You mention that the tweets are connected to the front speaker wires. Does this mean that there are a total of four wires going out of the factory amp for the front mids and tweets? If so, then where do the front wires get split to run the mids AND tweets? thanks!

Oh yeah, and are the sub outs on the other harness of the amp?

As far as the front outs, yes there are just four. A6 A13 A7 and A14.
According to the diagram, the tweets are split right off of the front speakers.
The woofer outs are:

A2 1(+) Brn
A9 1(-) Red

A1 2(+) Blu
A8 2(-) Gry/Blk

On the sub itself the wires are red and black though. So they apparently go to a junction somewhere.