If we play in a live concert, we have to consider how the sound of the organ is perceived by the listneners whereas in making a recording there is an issue with microphone sensibility to pick up certain sounds.
To illustrate the difference of these two situations, let's take an example of registering a chorale prelude "Ich ruf zu Dir, Herr Jesu Christ", BWV 639 by J.S.Bach from the Orgelbuchlein.
Although this piece can be registered in a variety of ways, a good option would be to play the right hand part on Oboe 8' combined with Flute 8' (with or without the tremulant). If you are playing on a swell division, the swell box could be almost closed. Of course, it depends on the actual sound of these two stops and how they balance with the left hand part.
The accompanying left hand part could be registered with Flute 8'. If this part sounds somewhat too weak compared with the right hand part, you can strengthen it with another soft stop of 8' such as Salicional 8'.
The pedal part sounds best if we use soft 16' and 8' stops, such as Subbas 16' and Flute 8'. These stops are usually sufficient for this kind of texture.
While this registration might work for a live concert or church service, we also need to be prepared to adjust it to work for recording. When recording, the balance also depends on the sensibility of the microphone. Some microphones seem to work better for higher pitched sounds.
Therefore, sometimes for the recording I strengthen the bass a little with an extra 16' or 8' stop which in live performance might not be needed. The left hand part is also important to be audible though not too prominent.
Since every organ is different, there are quite a few registration options with each instrument. The best way for you to go about this is to listen to 10 or more different recordings or videos of the piece, compare different registrations, critically think about them and decide what is your favorite and why.
You might find several versions you like really well. Therefore, you can play the same piece with different registration on the same organ quite successfully. Just give it a try. Remember, the more registration options you know, the better.
If you would like to know more about organ registration, I highly recommend The Registration of Baroque Organ Music by Barbara Owen. As Journal of the
American Musical Instrument Society writes, "In this book, Barbara Owen has
created a rich resource of historical information coupled with strategies for
interpreting that information on today's instruments."
Sixteenth Century Journal also adds that "... Barbara Owen has succeeded admirably in distilling three centuries of organ registration practice into a volume less than three hundred pages long.... Anyone with an interest in the history of the organ and its music... will not want to ignore this book." I personally use this book as a guide for most of my organ recitals.
By the way, do you want to learn to play the King of Instruments - the pipe
organ? If so, download my FREE video guide: "How to Master Any Organ
Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.