First, dont worry about any kind of factory plugs, the speakers wires will attach directly to the amp. The best way to configure this set up would be to wire the LT and RT bow speakers to chnl 1 and 2 of the Amp. Then wire the 2 LT main cabin speaker, in parallel (+ to +/- to -) on chnl 3, and the 2 RT main cabin speakers in parallel to chnl 4.
You will need to identify the + and - of each speaker, and make sure it will reach the amp when properly run, wire tied, and tucked up out of the way.
What sub do you plan to use on the class D amp chnl?
Are you using this amp to replace another? Sounds like you are moving the speakers from the head unit to a new amp install.
What size power/ground wire are you planning on using? What do you have in mind for circuit protection? You will need about a 50A fuse or breaker. I prefer circuit breakers myself.