The guy you spoke with at crutchfield shouldn't be giving technical advise, he was probably just a sales person who has no idea what he is talking about. Amplifying your stock speakers is a great way to get more volume and clarity on a budget. The stock speakers in our cars are pretty decent, better then most cheap aftermarket speakers actually.
You can use a single 4 channel amp to run everything. You would use the front 2 channels to power all 4 factory speakers, and bridge the rear 2 channels on a single 4 ohm sub (this is assuming the amp is 2 ohm stable, which most good amps are). I've done setups like this in dozens of customers cars with great results.