Rugwerk: two 8' flutes, two 3' nasards
Hoofdwerk: Salicionaal 8' and Gedekt 8'
Pedaal: Subbas 16 and Gedekt 8'
The reason for playing the cantus firmus on the bottom manual is that if the accompaniment is played on the lower manual, at certain points your arm will rub against your legs (in my case for sure), causing errors. So I found that the best way to have the left arm higher to avoid any interference of my elbow area with my legs.
Score used: Incoginta Organo, Volume 7 (Harmonia publ.), ed. by Ewald Kooiman.
Also on imlsp, version seems slightly different: