Upgrading the audio system

I'm looking to finish changing out the speakers in my '08 Silverado crew cab to something of better quality.I already have a different head unit,a Pioneer,and the front door speakers have been changed to Polk audios.I'm looking to add an amp at some point too to get the sound where I want it.
One thing I noticed after changing the front speakers was that there must be a factory crossover network.After putting in the new units I still had sound coming from the tweeters on the windshield pillars,of course I used the factory speaker wires too.Once I get an amp installed I'll be running new speaker wiring as well.
To make a long story short(er) should I go with 3 way speakers or just look for the more common 2 way?Given the facts that I'll be putting in an amp and new speaker wires at some point.