
With a puppy I would initially teach the sit only in sit stay exercises and not in the heel-work as an automatic behaviour on stopping.
As you are allowed to give as many commands as you like in Obedience until you get into Novice the automatic sit isn't really needed and would be a hindrance at first in the show ring until you have a confident show dog.
By that time you can go onto more precise obedience work and automatic sits and close heel work and the dog will know that the two kinds of work are different.
Use different commands for the obedience heel work to the show work, and some people use different leads, and your body postures will be different too, and the mature dog will know.
If you are a god trainer then you should be able to train both disciplines in tandem from the start without confusion, but for th average non competitive person I would start with Ringcraft and not include sit in the heel work at training classes for obedience.