When you auto detect the virtual keyboard or pedal board you press (on the physical keyboard) you are using the bottom note (you want to play) and the top note (you want to play); if the range you have selected is less than the number of notes for the virtual keyboard or pedal board, HW only responds to the range you have selected.
You could perhaps use the bottom octave of your keyboard for the pedal division and the remainder of the keyboard for a manual division (If you overlap the range then you can have both divisions played by the overlapping notes.)
Remember HW has an "auto pedal" facility which when engaged plays the lowest note of a chord on the pedal division as well as on the manual. (There is also a similar "melody" facility where the top note of a chord is played on the identified division as well as on the manual). See View| large control panel | master couplers screen .See pg 108 and following in the user guide...
BTW The St Anne organ includes both the "auto pedal" and "melody" functions set up for you to try out.
You can also use the floating division feature to change which manual division is connect to the keyboard at any one time....see the manual (or other forum threads).
Iain