no you can NOT just ground the parking brake wire, the unit needs to "see" the wire get grounded AFTER the unit is done booting up, the easiest bypass options are to either wire to a switch or get a PAC TR7 and program it to do the bypass automatically.
when you say "rear speakers" do you mean the actual rear speakers (in the rear doors) or the factory subs (in the rear deck) if your rear speakers are indeed not working, you messed something up in the main harness. if your subs are not working, then you need to correctly hook up that smaller harness, not really sure what is so confusing about it, it has RCA plugs for sub signal in, and then it has a blue/white amp turn on wire which the pioneer also has.
you will need a resistor to keep the subs from "popping" every time the car is turned on or off.
if you are still unsure of anything, i would recommend a lot of searching around, as there has been about a hundred double din install threads created with a lot of good pictures and step by steps. every question you could ever ask has been cover extremely well in those. most of them are about AVIC's but the install will be exactly the same as an AVH model, just no GPS antenna to run.