Excessive movement of a testicle, especially against the thigh, can lead to development of a "third testicle".
A doctor informed me that a lump I discovered after PBP-2003 and during a tour across Northern Europe was due to irritation of the vas where it connects to the testicle. The vas is the bit of tubing that connects the testicle to the body and, I think, is the bit cut and sealed in a vasectomy (hence vas-ectomy).
Pedalling in the bikeshorts I had at the time meant what must have been excessive movement of the testicle in question, and it tugged on the vas. The lump actually grows to be quite a size, and can even double the size of the original testicle... and feels like another one. Hence the description of a "third" testicle. The problem also can occur after a vasectomy because the vas becomes irritated (annoyed???).
The doctor said there wasn't anything to be done, then related how an Italian family had as its symbol, three balls for this very reason.
The position and/or looseness of the chamois also have have an influence on whether you get chafe on the glans, which can be very painful. If you have the early signs of chafing, it may require a simple rearrangement of the penis inside the shorts, or you may have to pull your shorts up so they are tighter around the penis, or simply replace the shorts. The problem is likely to become more prevalent when riding in rain.
I have found that cleanliness if very important, but sometimes on randonnees, it can drop down the priority list when battling against closure times for the next checkpoint. I sweat a lot across the top of the public region, and I seemed to develop a painful pimple on the left side where the penis joins my abdomen on rides over about 400km. I take wet wipes in Ziploc bags now so that when I use the washroom, I can at least wipe down that area to remove some of the sweat that is causing the irritation.
Getting a seat that suits you is great, and because we are talking Touring, it is nice to be able to ride without the need for specialist bike shorts. The problem with male (most) underwear is that there are usually seams that run right down the middle and correspond with centreline of the human body -- that is, the perineum. Chafe of the perineum is not pleasant. There are, I think, underpants that don't have these seams, but there are also bike shorts like underpants with insewn pads that work quite well. You get the benefit of padding, but don't have to reveal your Lycra.
As to chafe, I use tea tree lotion as a fast-acting agent to heal. It has germ-fighting properties, so it helps in both the prevention and treatment of saddle pimples.
If you are male, don't be afraid of trying out female stuff. I've had really comfortable bike shorts that were designated female, but the pad was fine. And I get cheap leggings from Target as my cycling tights -- they are made of Elastin and cotton, but a good enough for me in cold rainy conditions.
Oh yeah... and if you think the Brazilian look might be an option for you... don't.