I've only broken away from keys to play guitar a little so far on RB3, but when I have I've noticed that sometimes when I have to play a series of alternating notes, it highlights both those entire colors of the highway while I do it. It looks kind of like the drum fill for overdrive does, but just for those two colors. I haven't figured out why it does this. Anyone know what this means, and whether it has any impact on what I'm supposed to, and able to, do at those parts?

It's suppose to replicate a trill, but to be honest I have no idea how to work them so I just try to play the notes as they appear in the lanes and my combo usually breaks.

As the person above mentioned, it indicates a trill. What the highways represent is that so long as you "trill" the notes faster or at the same speed as they appear, you will maintain your combo.
 
It's there to make those sections a lil easier. That's all.

" As the person above mentioned, it indicates a trill. What the highways represent is that so long as you "trill" the notes faster or at the same speed as they appear, you will maintain your combo.  It's there to make those sections a lil easier. That's all. "

I haven't noticed it making those sections particularly easier, sometimes I keep my combo, sometimes not - but that was about par for the course in previous versions - I always had trouble with tracks like "Black Sabbath - NIB" which feature regular repeating trill sections.  I guess my fingers just aren't quite fast enough, or maybe its a mental thing.

Yeah, the mechanic is supposed to make it easier since real-life musicians have variations in the speed of their trills. The trick to not breaking combo is HOPO-ing it rather than strumming. It has definitely made my life easier.