Since we take sides in the civil war, which ultimately determines who rules over skyrim in the game, how would they explain this history wise in the next game?

Like what would they say about the events of the CW and who would they say won it in history books in the next game? considering the outcome is entirely up to us depending on who we side with

My guess is there will be a permanent truce.

Same as the outcome of all the other games, we will simply never hear anything about it ever again.

Excepting some vague rumours that are not related to our player character and a few books that describe what happened after the war.

The CW probably won't even be mentioned in TES VI.

It's only a sideshow in TES V, having nothing to do with the MQ.