Hello.
In HW pistons are associated with the sample set currently loaded. Many sample sets provide the pistons which operate in the same way as those provided on the corresponding real organ, so the pistons the sample set provides will operate on the same groups of stops as they do on the original instrument.
HW provides what it calls “master pistons” which can be tailored to do what you want (manual page 98 onwards). These are additional to any pistons provided by the sample set. You can set the scoped master pistons to operate on any subset of stops you wish. You may need to read the manual a couple of times!
Remember these are set up per organ and you have to do this for each sample set, and they are additional to any pistons provided by the sample set.
Iain