Hey everyone. First of all, thank you to rootsrat for telling me about S.T.E.P. I really appreciate all the feed back and it's given me a lot to think about.
When I was making the mod I originally used the Riften Sign post to hold the flags and it looked a little awkward. I settled on the civil war banners because I thought it was a better fit. I like to think the Jarls had a discussion in a previous moot and agreed to put up the banners and make them to a certain standard. The Eastmarch / Stormcloak banner looking newer was just a happy coincidence. I couldn't actually find a banner for Windhelm in the CK and the Stormcloak banner was the closest I could find.
I used Warburg's paper map when placing the banners to make sure they lined up properly. I'm a little bit OCD, so I wanted them to match up with the map lines as closely as possible.
I agree that stone markers would look better in some locations, however I'm not really sure what to use. If anyone can recommend an asset within the CK I'd appreciate it. I have zero experience with creating my own models and textures.