This is a common issue faced by many cyclists, including professionals. A well-known cyclist used medicine for his saddle sore to explain doping tracers found in his urine test. There are in general two types of saddle sore. One is caused by chafing between moving part of your body and your seat. The other is caused by lasting pressure of sitting.
Saddle sore caused by chafing can be remedied by choosing a seat that fit your butt. This is easy to be said than done. There is no practical way to know which seat would fit without using it. I’m still waiting for the modern technologies to be used to scan one’s butt and 3D print a seat specifically for it. Most riders know in general what brand/model, type, and shape of seats may fit them. There is always a breaking period that allows your butt to get used to a new seat. Some people claim that an unfit cycling short may also cause saddle sore. I didn’t experience that. Another common way to prevent and mitigate this type of saddle sore is to use chamois cream. It is to lubricate your butt. You may apply it to your cycling short or directly to your skin. The latter is much more effective. It should be used before the ride, and during the ride if needed. Another way to prevent and mitigate this type of saddle sore is to wear clean cycling shorts. This can be hard on a long-distance ride when washing and drying your shorts every day or every other day (you don’t want to carry more than one pairs of cycling clothes on a long-distance ride). Alternatively, you make sure your butt is cleaned immediately after each ride (hence the handy wet wipes if there is no shower). Bacteria accumulated on your skin may accelerate the development of this type of saddle sore and slow down its healing.
The second type of saddle sore caused by pressure is similar to bed sore. To prevent it from occurring, you release the pressure from time to time by standing up on peddles. It only takes a few second to let blood flow through the sensitive part of your butt. There is no other way to handle this. No matter now fit a seat is to you, sitting on it for hours day after day would make your butt hurt.
Training on long ride would help you prevent or reduce both types of saddle sore. This is an open secret: All serious bikers, professionals or amateurs, have calluses on their favorite spots of their butts.
Chidong Zhang's WA2MA Bike Trip 