I was thinking I would wait until I have done all the quests in every city, to make sure nothing is screwed up when I do those quests. But for all I know completing all those quests may affect the Civil war questline somehow if I do it after? If at least anyone could tell me when you start getting quests to take over cities that'd help.. then I could just do the ones up until then, and then save the rest for after I've finished all the cities.

EDIT: In case it matters, I will be doing the Stormcloak side of the questline.