I tried looking online but of course I got conflicting opinions so now that more time has passed I thought I'd ask again.Which is better to do first and why or doesn't it matter.Time for a bubble bath and a glass of wine.Talk amongst yourselves and I will check back

Hi Grace,
In 1000 hours of play, I've realized that the game is setup so the civil war will continue and not be resolved.
In both playthroughs I resolved the war, once for each side.
But there are loose ends (and some outright bugs) that indicate this is not what the devs had in mind...
So I recommend you do the main quest first.
Then, you'll be able to host the Truce Talks or whatever they call them, hosted by the Greybeards, with Ulfric and General Tullius together in the same room (which I have never seen).
Last time I saw Ulfric was in Sovngarde, heheh...
Anyway. Have you done other stuff yet (Thieves Guild, Dark Brotherhood, Companions)?
I have always saved the main quest for last, but would do things differently the third time through.
(But that's not happening anytime soon!)
Regards

Theres already a thread about this going on http://www.gamesas.com/topic/1357490-what-first-main-quest-or-civil-war/

I'm still confused.

Can I still do the truce talks (Season Unending?) if I pick a side?

If you side with anyone during the peace treaty, it will not affect your status in the Civil War at all. Though if you side with someone, General Tullius or Ulfric will chide you a little for not being wise enough to side with them. But it still doesn't affect the war, except for the swapping of controlled holds.