Here’s the “official” way to do this:

1. Approach the stall or urinal, but stop a step or two in front (space permitting—you obviously don’t want to get in people’s way in a busy subway restroom, for example). 
2. Bow discreetly. 
3. Clap your hands together twice (softly—again, you don’t want to disturb people). 
4. Lower your head for just a second and give thanks. This is kind of just a pro forma gesture, but the idea is you’re giving thanks for the liquids you’ve drunk (remember clean water used to be a lot harder to find), and the people who have provided the facilities, and the people who maintain them, etc. 
5. Use the facilities as normal. 
6. Step back, bow again, and go on your way.