I swear snake piss has got to be the worst thing I have ever smelled! But, I love them! I didn't throw out my kids when their diapers stunk up my house (don't get me started on the new dog and his amazing farting ability) I'm not going to do that to my snakes either!
The best way I've found is to clean it up as soon as you can after they pee/poo, take it out in a grocery bag to the trash outside, and clean the enclosure. It gets ripe sometimes, but the sooner you get to it the better!