I go through both chainstays, that way they cannot take the rear wheel off. You could go through the top part of the rear triangle too, either way as long as both sides are in the lock so the wheel can't be pulled through.
You don't need an especially long ulock, 8-9" should be enough to go through both and the large upside down U racks. Longer if you are going to take off your front wheel and lock it in the same lock. You just don't want to leave a lot of space in the u-lock since they can slip a jack in.
Locking skewers and a small u-lock would be easiest. Skewers aren't that expensive, esp if you plan on buying a separate chain/cable for the front wheel, might as well get skewers. I put them on my bikes, but don't want to go buy a small ulock so I am still using the big one and going through both stays just to fill up space to make it harder to fit tools in.
I lock it with the drivechain out, since often other people locking up their bikes will bump and move mine, and don't want it hitting the rack. I don't think anyone is going to be grabbing my derailleurs, not like i have expensive components.