I don't want to keep the factory amp at all. Want to change from 75 amp (stock) to 300 with the HW. Want to have the speakers in the leg farings and keep the other four (changed out to HW speakers too I am assuming). Then MAYBE (but probably not) have the option of removing the trunk for some rides which of course would remove the rear speakers. What would be the best way to hook this up (if even possible) to run 4 speakers when the trunk is off and six when it is on? 
If I may blunt, don't waste your time trying to do the 4 / 6 set up. Leave the rear speaker pods on for rear passenger controls, but forget about using the speakers. Turn the speaker boxes into cute little storage bins or ashtrays.
I honestly feel that after all of the work it would take to make that work out, the rear speakers just wouldn't compare to the front 4, and you wouldn't be happy with the outcome.
The only way I would want to do this, and I stress ONLY WAY, would be to contact Hawg Wired, and see if they can help you out with another pair of satellite amps and speakers, so at least it would be matched components, and not some hybrid system. This way, you'd be kickin it at 450 watts. A side benefit to a six channel HW system is that when you turn it up with a rear passenger, since they sit so close to the speakers, they might just get the "Big O".
Now wouldn't that make it easy to get permission to buy the HW set up?
Chief