I understand the 6x9s in the rear deck are considered woofers so if I replace them with a 3 way 6x9 will it get the correct signal to hear the highs or does the amp only send the low signal through that channel?
Yeah ^^ best to spend money on a true amplifier than on a 3 way coaxial 6 by 9 speaker set.
The pioneer speakers that come with the car will sound as if you got new speakers (unless you're an audio guy you prolly won't really notice that the speakers are same other than that you know that), being a good amount louder as well, assuming you install right with wiring and and amp and all that will hit the max RMS of them. Even if you don't hit that number, whatever it is, any amplification better than the factory pioneer wlll be a good upgrade, and would be, personally, my FIRST step towards a full sound system, along with a subwoofer.
If Bass isn't really your thing and you're satisfied with what you have in that frequency range, and also don't need or want it to be any louder than it is, and just want more depth, clarity, range, etc then yes upgrading the front component speaker sound stage with a quality set with separate crossovers will be the way to go. But keep in mind to most people's ears, to appreciate the depth of higher end speakers, power is the number one thing to have: an amp.
I'd go 5 channel amp, good DSP/Line out Converter, subwoofer, front component speakers, sound insulation, then 6 by 9s, then rear door coaxials, then a 2ch amp, lastly a smaller subwoofer in a sealed box (first sub as main in ported).
In that order, but some of those things you would install all at once ideally. That's kind of what Ive done, except I did up until the 6 by 9s at once. I am now on the 2ch amp and sub final part. This is just my own personal preference, choose what your heart, ears, mind, and wallet want!