Yea it's typical that most places use factory wiring for ur fronts. If you think about it, that's a lot of work for the installer to run a new set of spkr cables from the rear to the front, but it's worth it! I would honestly complain to the store and ask them to run a new set of cables. They'll give u dirty looks but come on u spent so much on it.

As for ur tweeters, so long as the crossovers and amp are hooked up correctly, u shouldn't be experiencing any problems! Exactly how new is this place? haha