Both will work.
However you run the risk of a ground loop or audio noise. I am guessing your amp will be in the rear of the car right (trunk or back of back seat)?\
So you are going PC, to amp, to front of the car, just to go back to the back speakers and back less to the front speakers. Everytime you have signal on signal action, you create a chance for no goodness to enter to loop.
So "will it work, and be ok?": yes
Should you? Might as well try, but if you get whining or bad audio, you may want to try direct to the speakers. Or at least direct from the amp to the rear speakers.