(Because this is a serious issue for many people, and I wondered if Mike and Claudia felt the same about multiple ring training, I asked her as well as Mike how they approached it.)
First, I do not believe that dogs are so stupid that they would not learn to recognize the differences. Obedience will have a choke chain, and a business like demeanor on part of the trainer, and the dog will pick up on that. In conformation everything is more relaxed, and even if using a choke chain, it is a much lighter type than the one used in obedience. In young dogs that are somewhat rambunctious, an obedience command will actually do wonders at times when moving the dog around the ring.
As far as the fear of sitting, oh well, just be prepared and it can be prevented. That of course requires that the handler pay attention to the dog. Maybe that’s why a lot of handlers prefer that the dog NOT be trained in obedience. I found obedience very helpful in nervous and insecure dogs and will use it as an aid for conformation training, since it seems to stabilize the dogs.
Agility comes into play a lot later as serious training, and usually does NOT create a conflict in regards to conformation, however sometimes refreshers in obedience seem necessary to gain or regain control and focus.