I have just bought a wiring kit for my car and it looks like everything is labeled on the wire harness to allow for proper operation of all aspects including the power antenna (just get any brand of wiring harness for your year from a local car stereo shop). I would think (have not done the change over yet) that you would have to buy a mounting kit too to get the new deck to fit into the dash properly. As you suggest, the Eq should be able to stay but you will effectively bypass all of the factory electronics (amp and Eq) using the new harness.

Hope this helps,

Tim