Here are few suggestion for playing organ pieces scored for 3 manuals on a 2 manual instrument.
Trumpet Tunes There are a number of trumpet tunes that are scored, or arranged for playing on 3 manuals. Some arrangements of Purcell and Clark follow this pattern. The typical set up is:
1. Trumpet stop
2. Accompaniment
3. Reprise on full organ.
On a two manual instrument:
Option A
1. Trumpet stop + full plenum, you could remove the trumpet when you play the reprise section.
2. Accompaniment
Option B
1. Trumpet stop
2. Accompaniment and add stops for the full organ section. This could be as simple as adding/retiring a mixture, or using a piston to make the change.
Toccatas Some toccatas have sections at three dynamic levels, for example, Gaston Belier’s Toccata pour grand orgue in D minor. On a three manual instrument it would be set up:
1. Full organ
2. Softer Plenum
3. Softest Plenum
On a two manual instrument I would have the softer plenum on the Swell and close the swell box for the softest section. You could also use a piston or add/retire a mixture from the 2nd section.
César Franck’ Cantabile has a section on Grand Orgue followed by a melody on the Récit accompanied on the Positif. If you have pistons available, you could have one set up for the Grand Orgue section and another for the Récit/Positif section. If you do not have pistons, you might have to add/retire stops on one manual for the Grand Orgue/Positif sections.
These are just a few examples. Hopefully others will offer additional suggestions.