My plan is to altanate main quest and civil war going main quest civil war main quest, depending which one has more quests. Reason I want to do it this way as I feel it would have a more natural progression in Skyrims time line. as opposed to they only bothered to fight the civil war until you finished the main quest.
Is this viable will it create bugs or make the story weird or not make sense? I plan on doing storm cloaks btw

These two quests are almost designed to work together. I still like keeping them separate.

However, there is no reason to not do them at the same time, although it might make more sense story wise to work on parts the MQ, then do the CW for a bit, then go back to the MQ. You will kind of figure out those points as you go along in the stories.

There's no 'almost' about it. Unfortunately, we cannot do the civil war without also beginning the main quest.