I go sans underwear as often as possible -- running shorts, gym lycra tights, biking shorts & jammies are all worn without underwear. As for cleaning the cycling shorts, I always just wash them on warm with Wisk and dry them on low in the dryer. They seem to do fine. I do think to avoid infections, you should take them off as soon as you're done and shower with an antibacterial soap.

http://www.drspock.com/article/0,1510,6235,00.html

http://www.drspock.com/article/0,1510,5355,00.html