Help please? Speaker install issue

The generally accepted rule is:
WHITE = left, positive.
GREEN = left, negative.
RED = right, positive.
BLACK = right, negative.

It doesn't really matter. As long as you have the negatives and positives lined up properly you'll be fine.

Just label your wall plate after you connect the wires. For instance label the top pair (the green and white wires) Front Left, the next one (the black and red pair) Front Right, the third row Center channel, etc.

You will have to run a new 2 conductor wire from your AVR's center speaker connection to your center speaker's terminals, with or without a wall plate in between.
I don't have any experience with a wireless center speaker connection, if that is an option at all.

What exactly is this room layout? Most people have the front and center speakers somewhere close to the receiver and TV and dont need any in wall wiring.

Is this current in wall wiring for surround speakers?

Most likely no. The Bose "receiver" is really only designed to work with their gear. The DVD player hooks to the "bass unit" and the speakers plug into that if I remember correctly. If you'd like to use the existing in-walls, I'd recommend going out and buying a new receiver.

YOU NEED A NEW RECEIVER IN ORDER TO USE THE IN-WALLS.

The 3-2-1 needs to be connected to the "bass module" and the speaker outputs from there are heavily equalized. So basically you could do it... but I wouldn't.

What you want to do and what you are able to do are 2 completely different issues given your current equipment. You may want to use in-wall speakers, but that Bose 3-2-1 unit is not designed to run any other speakers than the little cube speakers that come with it. It's designed as a stand-alone unit and not designed to be upgraded or modified. If you want to use in-wall speakers in a surround sound application, you need a receiver and speakers designed for that capability.

The Bose 3-2-1 system is designed as a simple to use plug-n-play unit that is suppose to simulate surround sound. It is marketed to the person who wants the home theater experience but who doesn't want to (or know how to) set-up a complete 5.1/6.1/7.1 speaker layout. Bose is known for proprietary connections that only allow the consumer to use Bose products. If you are happy with your 3-2-1 system set it up the way it was meant to be and enjoy it. If you want something more, you will have to spend more time and money to achieve that.