Yes, it would be better to run 6.5's in the place of 6x9's. There are speaker adapters that you can buy to make them fit.
The Alpine Type-R's are very good subs for their price range. A lot of people like them.
Can't say I really know what your talking about here: "what would be a good amp to run with those speakers with no subs and what size?" If your talking about your 6.5 speakers, then we'd need to know what the RMS is on them.
Run some components up front and some 6.5 midbass drivers in the rear with the proper speaker adapters. Run them off an amp that puts out about 150rms. Also sound deaden the door and rear deck pretty well.