If your bike shorts or MTB baggy shorts do not have a chamois, padded underwear can be worn to add comfort.
While you can bike without underwear in regular, non-padded bike shorts, the addition of the padded underwear, usually with gel or high density foam inserts, can help cushion your bottom and help you avoid sores during long rides.
The padded are designed to be worn like regular underwear, but they add protection and cushioning for when you are on the bike.
They do not look bulky under everyday clothing, and no-one know you're wearing padded underwear for cycling.