Change registration when structurally necessary. If there are no original registration suggestions from the composer, I suggest changing the stops only in places which are important structurally. Think about the form of the piece. For example, when playing a prelude and fugue, it is often OK to change registration or at least manuals after a prelude. However, some people change stops during the fugue itself. Although there is no right or wrong decision here, still, think about whether or not the registration change emphasizes the structurally important parts of the piece. I think that adding a stop just for the sake of sound is not as strong as changing the stop when you see the need for it (when the second subject comes in or at the start of a stretto section etc.)
Simplicity. In case of doubt, keep it simple. It is always better to play a piece with one registration throughout than to make things over complicated. In other words, if you feel that your prelude and fugue needs changes of registration because the sound of the principal chorus is too harsh on your organ, it is best not to bother with it, unless you are really confident of your decisions. Very often we think that listeners cannot stand this sound for a long time but in reality what is more important is music itself. A fine composition will sound well using several different registration choices. On the other hand, it is hard to make a weak composition more convincing by changing registration (it takes a lot of experience). However, in some cases on certain historical organs, the registration might be perhaps as powerful tool as the music itself. This is why much of early organ music might sound boring on a modern organ.
Another example: I know many organists who register the music of Franck in a very complicated manner. They try to achieve the perfect dynamics and add stops every few phrases. This is obviously too much. For music like Franck’s, we still need to clarify the structure of the piece.
Practice over theory. This is very important: no matter what the original composer’s indications are, still we make our decisions based on the result. For example, if a French Romantic composer wants an oboe for a particular place, we have to think what kind of oboe was available to him. Then we need to check whether or not the oboe on our organ produces the same effect. Or in another case, if the piece from French Classical organ school has very specific registration indications, such as Voix humaine (a reed stop), we still have to compare the French sounds with our organ. A German Vox humana would not be the same. In many instances, we will have to make compromises in order to achieve the desired result.
Use 8’ or 16' as foundation in the manuals. Regardless of what kind of registration you choose, it is the most common to use 8' stop as the lowest sounding stop in the manuals. However, there are also many instances where 16' foundation in the manuals is also advisable, especially in Organo Pleno registration on large instruments. Sometimes mixture stops are constructed on the 16' basis. For example, it is quite common practice to have a low mixture in the Great. By low, I mean it is based on 5 1/3'. In this case, we have to use it always together with a 16' stop. Other mixtures are based on 2 2/3' or higher. In such case, 8' stop as foundation would work just fine.
Use 16’ as foundation in the pedals. For majority of music written after 1700s, it is normal to use 16' as foundation in the pedals. If the manuals would be based on 8' level, the pedals would be one octave lower. In other words, if the lowest stop in the manuals is 8', play with 16' in the pedals. Playing without the 16' in the pedals would lack the necessary gravity.
Exceptions. As with majority of rules, there always are exceptions. For example, it was a common practice in the Baroque period, especially in the 17th century to play the cantus firmus (the chorale tune) in the pedals, even though it would be notated in the manuals. If the choral would be placed in the tenor voice, you would need to use 8' as the basis in the pedals. If the cantus firmus would be in the alto, you could place it in the pedals with 4' registration. Moreover, choral tune in soprano could be played in the pedals with 2' registration.
By the way, you could try to play hymns this way. This would make a fantastic sight-reading exercise. Here you would need to have alto and tenor in the right hand, bass in the left hand with 16' on a different manual, and soprano in the pedals with 2' solo stop.
These are my personal suggestions for registering an organ composition. Of course, this is just a generalization and you have to consider many variables, such as historical period, national school, type of organ music, instrument available and many other things. 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.