I hate touch-screens – I just can't get on with them – they feel completely wrong. So I use ordinary monitor screens (BenQ), and set up combinations using a trackball (I hate mice too!). Once a combination sounds right I save it to one of the Stepper General pistons – there are a thousand of these available, quite enough for a complete recital, and they control the whole organ with one press. Further sets of 1000 can be saved if required.
My keyboards don't have pistons, so I use a couple of keys on the lowest manual to step forward or backwards.
Hauptwerk offers plenty of ways to control stops and combinations – a qwerty keyboard for instance, a Launchpad, or the Behringer equivalent (which is cheaper, but I can't find the post in which this is mentioned).
Any of these methods will work reliably, provided you use the Backup function on the File menu regularly to save what you've set up. There's no right or wrong – whatever works for you, and feels comfortable, is fine