Yes, one can still use the manual controls after having applied the auto upright feature. Here are two tutorials that I found helpful (look for the Upright tutorials in each link). Be sure to note the addition of the new Aspect tool which can correct for the lengthening of the height of key stoned buildings.Julianne KostLaura Shoe
Though if you are going to do that, I think it's best to undo the auto upright and start from scratch with nothing having been done in the background, it's not really any more work. I'm not sure the interaction of the leveling and the vertical changes of the auto controls is the same as that between the manual vertical and rotation controls based on what I've seen. BTW, the Kost tutorial a really good intro to the tool (but then, I am a Julianne fan anyway).