I am on season unending quest and I have completed the peaces trance.

I wish to know, when I have completed the main quests, could I start the civil war campinge?

Or should I had completed the civil war campinge before starting the Season Unending Quest?

Finally, by giving up some of these towns away to certain sides, would this effect the quests available from these town?

Thanks.

You can still complete the Civil War questline after you finish the MQ.

And as far as I know, you can still complete the quests from various towns, the only difference will be the Jarl giving you some of the quests will be different.