I'm somewhat 50% into the game. I've done a good portion of the main quest and have done a lot of side quests in major cities as well as completing the Thieves Guild and Companions. Now i'm stuck, im not sure if I want to finish doing all of the side quests first or finish the main story then do the side quests. I remember in oblivion, I did everything there was to do in the game including expansion packs and then finished the main quest last and regretted waiting because i didnt even use the armor in the end because it was weak. I wan't t go ahead and finish the main quest because its getting really good now but i'm afraid i might end up voiding certain quests if I end up finishing it. The same thing can go for the civil

I'm sorry that I have to be a stick in the mud, buddy, but like the Moderator said inhttp://www.gamesas.com/topic/1328389-things-to-do-before-completing-the-main-quest-line-or-civil-war/, you should use the Skyrim Cheat, Hints, and Spoliers forums regarding your question.

Then again, I'm a noob here, so what do I know?

Anyways, have you joined the Dark Brotherhood? I hear that their questline is pretty exciting.

You can do what ever you want. You don't even need to do the civil war quests. You can do it first... your can save them for later. You can finish one line of quests before starting another, or run several at the same time. There's nothing you can "wrong" to spoil anything.