Use rests for registration changes. The best places to change registration using toe studs are the spots with rests in the pedal part. The rest is necessary to press the toe stud with the foot. For example, if the registration change is needed at any specific place and you intend to do it using toe studs, locate the rest and press the toe stud with the left or right toe, whichever is more convenient for you. However, it is better to use combination piston if the rest is in the hand part.
Determine which foot to use. If you see an appropriate rest for pressing a toe stud, look on which side this stud is located. If it is located on the right side of the organ, press it with the toe of the right foot. Similarly, if the toe stud is on the left side of the organ, it is better to use the left foot. If the toe stud is around the middle of the organ, you may use left or right foot. However, there might be some cases were it is more appropriate to use the right foot on the left side of the organ. Study the pedal part and you will easily understand which foot is more comfortable to use.
Use the free foot in places without rests. If you absolutely must use toe studs and both hands and feet are busy, use the foot which is not playing at the moment. For example, if on the spot where registration change must be done you play with your left toe press the toe stud with the right toe. Similarly, if the right foot is busy, use the left foot.
Adjust your pedaling. When you write in pedaling in your score, always take into consideration the use of toe studs, if necessary. It is much better if you plan for it from the beginning. However, sometimes you will need to change the pedaling according to whichever foot is more appropriate to press the toe stud. Do not hesitate to make these changes because they will help you to change registration more smoothly.
Prepare in advance. Just like in pedal playing it is best to use pedal preparation, you should prepare for pressing toe studs before the actual spot where registration change is needed. Try to place the foot intended for registration change on the specific toe stud as soon as this foot is free to move. In other words, as you release the pedal with that foot, move it on the stud in an instant. Such preparation will greatly facilitate registration change and you will not have to think about it when the actual moment comes.
Practice repeatedly. Any registration change must be practiced over and over until it will become automatic. Take a short fragment, like one measure before and after the change and play it in a slow tempo 10 or more times. Omit the hand part first and practice only the pedal part. Later, play the entire texture in a similar way.
Imagine the toe studs and practice. If you intend to perform your composition on an organ with toe stops but only have a small organ available for practice, you can imagine the toe studs on your organ. Pretend that the toe studs are located either on the left side, right side or the middle. Make appropriate movements with your feet regardless whether or not they actually exist. The sound is not important here but your physical movements are, so that when the time comes to perform your piece on the organ with the toe studs, you will be ready.
If you follow my suggestions and incorporate registration changes using toe studs in your practice, this task will not be as difficult as it might appear at first. One thing that it is becoming apparent here is that we cannot take the registration changes for granted and hope that when the time comes we will successfully press that toe stud. The skill of changing registration, like hand or feet coordination must be practiced as a drill until it becomes automatic. If you achieve the level of automation, you will have no difficulty changing registration by yourself.
If you would like to know more about organ registration, I recommend a treatise by G.A.Audsley "Organ Stops and Their Artistic Registration".
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.