Can you? Yes.
Ok to? Yes.
Recommended? Not so much.
Why? The OEM h/u is only 18W (maybe 20W) per channel versus amp @ 40W. So you will have an automatic imbalance there... The imbalance is fine electrical-wise but effectiveness of your rear speakers (which candidly is already low w/ 2.5-3" drivers) will be greatly reduced assuming equal sensitivity, etc.
Running wires from rear to up to the dash is the harder part. Thru the firewall to amp is a piece of cake - the grommet is there just a quick "x" cut w/ a utility knife. Suggest you either find a 6x40W amp from a 996 or one from another 986. From there it's a quick drop in. Otherwise, replace w/ an aftermkt amp (my recommendation - though OEM will be sufficient)... (If you haven't already, replace the garbage component speakers Porsche stuffed in the dash.)
You're doing all the hard stuff to make audio system a much better sound stage... don't cut an easy corner as it's effectiveness is equally if not more important (and you'll most likely double back later and correct...).
Good luck
