Nickel-based batteries are the ones that need to be fully discharged. Lithium batteries, which the DS uses http://www.nintendo.com/consumer/systems/dslite/battery_faq.jsp#dispose, do not need to be fully discharged. In fact, if you fully dicharge a lithium battery you will decrease the life of your battery. Here are several articles that discuss this very thing.

http://www.computerworld.com/blogs/node/521

http://spicygadget.com/2006/12/24/guide-getting-the-most-out-of-your-lithium-battery/

Like another post earlier the 500 charges are full charges which means if you do partial charges you will get more. I would personally recommend that you start charging when you get the red light so you don't accidently drain your battery and damage it.