I tend to have a mix of logic, semi-logic, inconsistent “logic”, consistent, and ad-hoc coloring. 
There are certain instrument groups that are in almost all my projects, that I am very consistent in coloring: Drums are red, bass is blue, acoustic guitars are yellow/gold, electric guitars are green, lead vocals are violet, and background vocals are magenta. The logic in those assignments? A somewhat hodgepodge mix. I really have no idea why I arrived at red for drums (maybe the drum set we had in my parents’ basement was red???). “B” for “bass” and “blue”. Most acoustic guitars have a yellow-ish face. “G” for “electric Guitar”, “V” for “vocal” and “violet”, and magenta is the closest to violet in the Cubase color palette.
There are others that I have in some combination almost every time or frequently where I’m less consistent. I have piano in almost every project, but I’ve varied the color. Sometimes I make it teal, which is the color I most often use for synths (which I don’t have as frequently), sort of as a keyboard group, but, if there are a lot of synths, I might choose a different color for the piano, with that color depending on what else is available and stands out enough from other colors. If I’ve got an organ, it’s likely to be orange (take a letter off the end and move one letter and…). If I’ve got strings, I’ll tend to use the closest color to brown (but it tends to look fairly orange in some of the uses), brass would likely be some gold-like color, and woodwinds tend to be more or less miscellaneous colors, depending on what is available (except sax would be the same color as brass since I’d mostly be using that in a trumpet/sax/trombone brass section). Percussion would probably be pink (a combination of the “P” connection and that it’s a lighter red, thus close to drums in that sense).
Okay, so kind of all over the place.
One thing I am pretty consistent on, though, is that the submix buses for any given instrument group are the same color as the instruments within the group. If that group also has effects buses in it (e.g. drums and lead vocals almost always do), they’ll also have the same color, or possibly a lighter shade of that color to help me quickly distinguish the FX from the tracks. As for multi-instrument subgroups, like instruments submix, mix bus, rear bus, and master, I usually just leave those the default track color, and those end in a different zone in the MixConsole. Or, for some related instrument groups, like a drums and percussion submix, I might use a shade between those of the groups.
I don’t use project templates since my projects have mostly been pretty different from one another in terms of which actual virtual instruments get used in some of those basics, but I do tend keep the same, or a similar, vertical track order for those groups, for example, with drums at the top, then percussion if it’s there, bass, acoustic guitars, electric guitars, piano, organ and/or synths, brass/strings/etc. if used, background vocals, then lead vocals. FX and subgroup buses are with their related tracks, or after all there components (e.g. in the case of an instrumental submix), and main mix, rear bus, and master (Stereo Out) are at the very bottom, but I use the visibility zones in the MixConsole to put key buses in different zones.