Is it a good idea to use regular speaker wire(the stuff that comes with the speakers) for this project? Or should I upgrade to a thicker wire.

My setup is going to be a 4 channel JL audio amp, with 75 or 100 watts in each channel. My door speakers are going to be Boston SL65 componets, while my subs are two JL 6W0's in the rear seat area.

I typically run 16Ga wire for most speakers (Subs I run 12Ga typically)... I think most of what comes with speakers is pretty cheap stuff; I don't use it for speaker hookups, but it probably could be without too much problems.

yeah use 14-16 guage wire for your components and about 12-14 to wire your sub-amp . for the amp you should use atleast 4 guage power wire and probably the same guage for your ground you might get away with 8 guage ground wire
EDIT: on second thought use atleast 4 guage for your ground also