You keep track of timeouts how?

[Nevadaref]

In the end, all of this comes down to everyone doing their jobs and in a perfect world doing them without error.
The problem is that errors do occur and as an official, particularly if one is the R, it is important to know how to proceed when an error occurs.

This is something which separates officials from each other. How they proceed in unclear or problem situations. Your top guys handle them well and to the satisfaction of others. Lesser officials will not worry too much about it or point the finger at someone else.
I try to have someone on the crew with definite knowledge. If I can obtain that knowledge and fix the situation, I will. My best defense to such problems is to be prepared.