Wear the "toilet" slippers. When in someone's home in Japan, it is common for you to remove your shoes and wear slippers. The same is to be done when you are going to the bathroom as there are usually a pair of slippers specifically for the toilet area that must stay there at all times. Remove your first pair of slippers, and slide into the second pair. (Of course the trick is not to let your feet touch the floor!)
Squat facing the door. This should be fairly self-explanatory, but squat so that your butt is facing the back of the toilet and you are facing forward. This may be little tricky, especially for females wearing dresses or pantyhose. Do the best you can and squat as a catcher would in a baseball or softball game.
Complete your business. The function of a toilet in the Japanese culture is the same as in America.
Use the candy-cane! There is a button on Japanese toilets which looks like a candy-cane (if you're lucky there will be an English translation.) This is meant to refreshingly squirt water in your private area to help it become clean. Be aware that when you press the candy-cane, water will shoot up from the bowl.
Flush. Some toilets in the Japanese culture have the good old American style handle on which you push down to flush, while others simply have a button. After you've completed your business, look for the button which does not have a special notation. This is most likely the flush. (Again hopefully your toilet will have English translations, but truthfully you never know.) Congratulations! You are assimilating to Japanese culture and have just learned how to use a Japanese toilet!