What do I do?

[rfp]

In one of the HS leagues I officiate, the home school wears dark and the visitors white. That's just what they do, I don't know why.

In this case, I would mention your observation to the R. I'm 99% sure he'll pass on it. If you were to override him in this case and whack both coaches, as a brand new varsity official, I think that's suicide. If anyone asks you why you let it go, you can rightly say you brought it to the attention of the more senior official and he decided to let it go (for whatever reason). Then it's his issue. I think you get in more trouble for crossing your partner(s) in this case, than for sticking your neck out to enforce a rule like this. JMHO.