1st year ref dilemma! Pick up flag?

[oncelost77]

First of all, I love the forum and it provides great insight for a first year ref.
Well lets get right to it, I have been asked twice to pick up my flag by the head referee. In both situations I was correct, double forward pass and twelve-men illegal participation. Being a first year ref., I don't see a need in battling with my head referee over this. It is JV ball, not Varsity or higher. However, I do feel awkward picking up the flag. If anyone has insight and/or advice it would be greatly apprciated. In both cases, the referee later told me I was right.
My major question is what is the protocol for this situation. Do I waver and pick up the flag, or .... I am not sure of options here. Thanks in advance
First Year and Lovin' it.