Every captain I've flown with have their way of doing things. Not always exactly by the book. As long as those are just minor deviations that aren't safety related, I let it pass without giving it a second thought. From the list that would involve things like proper door opening procedure, not climbing all the way to optimum FL, no arrival briefing (when both are familiar) etc. If I have any questions I will ask, otherwise wake him up at TOD. A certain captain is known for reporting people for silly things... not exactly a treat to fly with him. Not the type of reputation I'd like about myself.
Without stepping on their toes too hard and challenge their authority, there are obviously times when you have to put your foot down. It has happened a few times and usually leads to a pretty tensed day with not too much chit-chat. Not that it has to be, but the tensed environment lead to a break down in communication and CRM. Some people have a very task orientated style, some are more person orientated. Dealing with SOP adherence I think requires a little bit of both.