1. Make sure the bicycle fits and is set up correctly for you.
2. Develop a strong core so that you sit on the saddle lightly (sort of 'perch' on it), and so that you sit with good posture. You should not have your full weight on the saddle. You should be able to distribute your weight between your butt and your feet.
3. Ride lots, do lots of other exercise as well (cross train), and become fit. Improving your flexibility, especially the flexibility in the lower back and hamstrings, also helps. Doing these things will help you feel more comfortable on the bicycle for longer periods of time, and will also help you distribute your weight on the bicycle.
4. The saddle you choose should be wide enough, but not too wide, for your sitbones. Find out how wide apart your sitbones are, and determine how wide your saddle should be. Your saddle should also be the right shape for you ... flat, curved up in the back, or whatever. When you try saddles, try several shapes.
5. Extra padding on a saddle or in cycling shorts does not necessarily equal extra comfort. In fact, it often means quite the opposite. With extra padding on a saddle, you sink in and there is extra pressure and friction. With extra padding in cycling shorts, there's an increased chance of bunching, causing friction points. Many of us can ride comfortably with no padding at all, either on the saddle or in the shorts.
6. When it comes to shorts, make sure they fit well ... snug, but not too tight. If they become loose enough to start shifting around, you'll have friction issues. If the shorts have padding, make sure it covers your sitbones. Make sure you are not sitting on the seams, or that the padding doesn't actually cover your sitbones.
Once you get it right, you should be able to ride 100 miles, 200 miles, and longer with little to no butt problems.
I've covered 135,905 km in the past 21 years including 155 rides of 100 miles or longer ... and those 155 rides include not only centuries, but numerous Super Randonneur series, one 1000K randonnee, and four 1200K randonnees. In all that riding, I have only ever had one saddle sore, and very little in the way of saddle-related discomfort.