You're blaming the wheels for flats, but you're not sure if rim tape should be used? Please venture over to the bike maintenance forum :/

Edit: to possibly answer your questions:

Yes, use rim tape, or you're going to get flats.

Yes, the tires that come stock on most bikes are generally not the best.

I'm still not entirely sure if you're disappointed with the wheels or your tires, or the cause of your flats.