My boss is a civilian (a PG-05, which I am told is the equivalent to a Major). And if you go up high enough, I work for Dan Ross, who is ADM(Mat), a civilian. There are several military officers in between my boss and Mr. Ross.
He writes my PER, but there are varying opinions as to who signs it. He signed it one year and the LCol signed it another year. Some will say that a civi can't sign a military PER. My reading of CFPAS says he can, but whatever.
In our case, my CO is military, and I would imagine that, as an officer, most of the challenging issues (ie discipline etc) if they came up, would be dealt with by the CO. Less formal stuff - counselling, PDRs, and so on would be handled by my boss, more formal stuff, up to the CO.
For example - my CO signed my TOS recently, which would be the CO regardless, not the immediate supervisor.
You think we're bad for rank stuff - you should see the unions fighting over who should work for whom!!! We've had to re-work our entire org chart, because PIPSC (union) said that an ENG-05 can't work for a LCol and an ENG-04 can't work for a PG-05 or a Major. Our org chart is now one deep and a mile wide, cause we have so many engineers, and they all have to work for the Col (or something). They seem very very comfortable with the concept of rank and Chain of Command :