Everything in the EU says they last for a VERY long time, but I don't see that happening. I don't think we will see a lot in EP2 but more in EP3. Of course, there is a story to be told so maybe a lot of the fighting will take place between films, but I hope that doesn't happen, I want to see General Kenobi in action.
I think that the war will break out at the end of Episode II, with Anakin leaving as a young idealistic padawan and then we will return two years later, in Episode III to see the jedi ranks massively decimated and Anakin a battle scarred, war weary veteran about to enter the final climactic showdown on Alderaan.
clone wars
I think the clone wars will start at end of episode 2 , and the end of them will occur near the start of episode 3 , right just before anakins turn. doesn't OBi-wan describe anakin as a hero of the clone wars to luke in ANH? This implies they must end before anakins turn. I can imagine the opening scrawl of episode 3 being something like' the clone wars are almost at an end, the jedi are close yto victory but at a great cost etc etc etc)
Re: clone wars
this is an interesting passage which i found at the beginning of SW:Technical journal of the Imperial Forces, under the heading, "A brief history of the Empire":
"The jedi were systematically hunted down and summarily executed. The jedi found themselves being abandoned, betrayed and even murdered by those whom they had protected for so long."
I believe that Palpatine will somehow, after the Clone Wars, turn the galaxy against the jedi and have them branded as dangerous outcast's, with Darth Vader probably betraying and then killing the high council members.