When I'm using Ezio's Eagle Vision (which at this point is only when I'm identifying a Templar Captain), sometimes I see paths or trails on the ground in either red or gold. What are they? Do they have to do with identifying the captain? Or are they just explained later in the game and I haven't gotten there yet?
I'm not really sure of how to word this nonconfusingly, so I'll just take a stab at it - just like your targets are color-coded in Eagle Vision, so are the places they've been. So, red trails mean a guard has been walking there (and probably will be again soon if you hang around) so this gives you some indication of the relative safety of a location in a broad sense.
Mobile mission targets, as well as captains, show up in gold - there are a few missions where this is pretty much the ONLY way to reasonably track down your target. (Two of the Master Assassin missions I've done so far, I think would be basically impossible without it - the first of these that I did tipped me off that I should follow the trails, though.)
This is easiest to observe in any mission where you have a companion who follows you around - they're gold, and you can see them leaving a gold trail behind as they walk around.