Why settle for Czerny pablum when there's so much good music to play? That's much more rewarding, and even simple good organ music gets you used to how, in pieces that you'd like to play for others or even just for yourself, the sound and touch and patterns differ from a piano.
In particular, arpeggios and broken chords are common in piano from Bach's sons to Liszt, because the piano has a damper pedal and doesn't have an infinitely long sustain. But an Alberti bass on the organ sounds ridiculous. (Vierne's occasional noodly textures aren't so much broken chords as tremolo or timbre. Because reverb.)
Another trick, because there's no decay, is squirming your way up and down. You can (slowly) play a legato C major scale with just the outermost inch of your thumb. This kind of stuff appears in polyphonic "choral" writing... which is common because rapidly changing between 3 notes sounding at once to full chords in both hands, as in Beethoven's piano sonatas, on the organ means a drastic change of loudness, whether you want it or not.
To train your ear that, unlike a piano, a high pitch might be quite far to the left, choose (say) a 2' solo stop for left hand melody, and quieter 8' and 4' stops for right hand accompaniment.
If your piano training included the Goldberg Variations, try them "with one or two claviers" as marked for each variation. The hands cross each other, but on two manuals they don't get tied into knots, BUT the lack of knotting can melt your brain. But3 in the meantime you get to master great literature.
When you get a pedalboard, your biggest hurdle will be independence of feet and left hand. It's an immense relearning to discover that your left pinky can have nothing to do with the lowest note.