i havent started the civil war quests yet but what i was wonderin was if i side with stormcloaks then will i get attacked on sight in Imperial controlled areas

No you won't.

If you mean imperial-controlled cities then no.

so they just cant tell what side im on i can still talk to them and all

They didn't really try very hard to make this "civil war" feel very much like a war. At least not as far as you (the player) is concerned.

I sided with the Stormcloaks and helped them out with the first mission, but after reading a book about the Great War, I changed my mind and wanted to go to the Imperials.
So I ran off to the general and talked to him. No option to defect to them or something, but he said that the war would only be over when Ulfric was dead.
So I figured I'd just go kill Ulfric in his castle !
I run off to Ulfric, get him alone in his room and just proceed to unload chain lightning on him until he.... falls to his knees panting...
Great, he's immortal. Also, after recovering he greets me saying "My friend!" .... >.>

wow ok thats good to know

Well, if you're a bit deeper in the empire quest line. (Or even finished it) And then try to run straight into the stormcloak camps they tell you to "Back off" and start shouting warnings. If you try to speak to them they'll attack you.

so no to camps but all cities will still be accessible like normal