I've been to Auschwitz & Birkenau twice, once with a friend when backpacking the continent and again w/my wife when we backpacked through the region....
The first time there we got there by taking a bus from Krakow's main bus station - not a tourist bus, just a local only bus to Oscwencim (the Polish name of the town).
The second time I believe we found that the local bus times didn't work for us, so we took the train from Krakow Glowny station to Oscwencim. From there, we took a local bus to the main entrance to the camp - Auschwitz.
I'd personally advocate, based on that, just taking local transport to get there, why pay more for a "tourist" service, when you can get there like the locals would.......
As far as the amount of time you need - I think we went in the morning around 9am and returned by 4-5pm. The "main" camp - Auschwitz I - has the museums, videos, and some guides who might walk you around and give some true gravity to the place.
Then you want to catch the bus to Birkenau, or walk the 1-2 miles to that camp. The moment you arrive you'll know you're in a sad sad place. I can't explain it, but the camp enterance there, and the whole place feels like no where I've been. I just spent 2-3 hours walking around the vastness of the grounds and absorbing the feeling. I still vividly remember listening to an old Jewish man who was back with his grandsons telling them how HE was unloaded from the train cars and explaining the place to them. I can't even imagine how hard it must have been for a man like this to return to a place of such sorrow.
One thing that struck me was that there are new homes being built overlooking the Birekanu camp. Can you imagine that?
But I'm rambling. Just be sure to go. While not pleasant, it's one of those experiences that will stay with you.
-A