That is the same problem I had when I tried to manually advance the civil war in order to do it without doing the main quest as well. It left me stumped. I don't know why they insisted on using the same quest for both sides, and I don't know how the game tells which side you are on.

Now that I think about it, I believe they used a single quest for taking every hold, on both sides. That is why you didn't see the name Whiterun. It is a screwed up mess, why Bethesda did it that way is beyond me. I imagine it was just to make it difficult for modders.
This post has been edited by SubRosa: Apr 19 2015, 01:17 AM