I got caught with this when I started playing midi files on Organteq and had the midi parts come out on all the wrong manuals.
You can see the default manual midi mappings for Organteq if you click on "Midi Mapping". In the pop-up window select "Current Mapping Preset : "One keyboard simple (attached)", which should be your default option, or click on the faint grey triangle on the bottom of the box to see the possible options, and select the "One keyboard simple", if it is not.
You should see a single keyboard displayed with the following data above it;
"Grand Orgue Any Channel Transposition : 0"
If you left click on "Grand Orgue" you will get a drop down list of "Récit : Grand Orgue : Positif : Pédale". Click on Pédale to select it and the data line will now read
"Pédale Any Channel Transposition : 0"
and the colour of the keyboard and the data line will change from blue to green The Pédale manual is now set as your default keyboard and will receive input from any midi channel number. Your midi file will now play only on the Pédale manual.
You may need to click on the "Transposition" box to select either "Transposition : -12" or "Transposition : 12" to get you notes centred on the Pédale keyboard, but this probably won't be an issue with you, as the music is written for the Pédale manual.
If you now click on "File : Export to audio file", or press "Ctrl + E", then choose where you want to save the audio file and in what audio format, your loaded midi file will now record as purely a Pédale audio file.
I hope that this helps you somewhat. The Organteq user manual, whilst far more comprehensive than most user manuals I have had to work with, does, however, assume some prior knowledge on the part of the user. No user manual is ever totally comprehensive, unfortunately.
Remapping the midi channels for a "Four Keyboards" current mapping preset, so that Organteq would correctly play other midi files was a rather arcane art, as most midi files number their voices in reverse channel order to Organteq. I still invariable forget and have to dive back under the bonnet to reorder the Organteq manual midi channel numbers in order to get sensible music.
Have fun under the bonnet.
Michael
Pianoteq 8 Studio plus all Instrument packs; Organteq 2; Debian; Reaper; Carla