In, say, Kontakt you could probably only have some preset registrations.
Hauptwerk sample-sets usually have samples for every single key and every single register, so you can combine them, as you like. Organs have registers that can be used in arbitrary combinations - which is usually pretty difficult to model in standard samplers. The sampler used in most professional software environments is probably hauptwerk (the software itself is free,, you have to buy sample sets though). I can’t give you any advice about creating samples, only about pipe organs and using sample libraries from the perspective of a player.
