I am installing a set of 6x9's in me 4kq along with a 200w amp. My question is, can i also use the stock speaker wires coming from the head unit along with the wires coming from the amp to power the 6x9's? I have only ever hooked up subs to an amp and never regular interior speakers. If i can, how would i go about wiring them. thanks for all the help.

Do you mean unplugging the stock speaker harness and connecting it to the amp speaker outputs?
You can do this no problem, so that you don't have to feed new wiring into the doors, but it is frowned upon as you should be using quality cable all the way to the speakers.
If you mean running the output from your head unit in conjunction with the output from your amp to the same speakers, then definately NO, unless you want to blow something up. Why would you want to?

....in my ignorance I though that I could get 50w from the head unit and 200w from the amp and put them into the speakers...but i guess i can't