The open-source reader "Evince" has worked very well for me, using a separate monitor oriented vertically, and a separate mouse hooked up to a knee lever under the keybed. When I've got the organ set up and ready to play, I click on view / presentation mode and position the mouse pointer somewhere on the page; this makes Evince the active window, but no midi functions (presets, stop buttons, etc.) are affected as long as you have mechanical midi controls for them. If you need to click on anything on the Hauptwerk screen, of course, this changes the active window and you have to minimize Hauptwerk to go back to reading the score.
I used Plural Input for a while, which allowed me to dedicate the 2nd mouse specifically to the 2nd screen; then I was able to use the touch screen controls for Hauptwerk without interrupting Evince. However, Plural Input seems to slow things down quite a bit (even though playing doesn't seem to be affected) and since my computer is not state-of-the-art, I decided to just stick with switching the active window, as above. It all works very well - until I go back to sheet music and keep whacking my knee on the keybed.