I found the answer, pretty simple:
Parameters for 'MIDI Parser':
midi.upper.channel I (1)
The MIDI channel to use for the upper manual. range: [1..16]
midi.lower.channel I (2)
The MIDI channel to use for the lower manual. range: [1..16]
midi.pedals.channel I (3)
The MIDI channel to use for the pedals. range: [1..16]
Manual 1 uses Channel 1
Manual 2 uses Channel 2
Pedalboard uses Channel 3
Since my simple controller keyboard has no facility to change the channel, I installed the virtual jack keyboard
where I can set the desired channel and switched it in between the organ input and MIDI keyboard output:

Unfortunately jack keyboard
can not split the keyboard. I worked around it by starting two instances of it, one using MIDI channel 1 and the other one using MIDI channel 3. There is some overlapping unfortunately but like this I can play the pedalboard with the low keys and the upper manual with the higher keys. (HuaXing is the output of my hardware controller keyboard):

UPDATE: inspired by --> Toms answer <--
with the application qmidiroute
— a MIDI event processor and router — the organ manuals can be accessed in any way that is within the range of the hardware keyboard. Since qmidiroute
does not supply jack ports it needs to be combined with the ALSA to JACK MIDI bridge a2jmidi_bridge
.
Here is an example using the two low octaves of the controller keyboard for the foot-pedal and the the higher octaves for the upper manual (since it is a small keyboard the low octave of the upper manual is skipped):


(HuaXing again, is the output of my hardware controller keyboard):
