There are a lot of battery myths out there, however the newer Lithium-Ion batteries (of which the DS and DS Lite use) aren't really affected by inconsistent charging. Not needing to fully drain the battery before charging is one of Li-Ion's best features. In fact, if anything, it is recommended that you charge it more often, not less.
I use my DS Lite every single day and my recharge routines are about as inconsistent as it gets. I never specifically wait for the red light before charging, and I often play while it is recharging. The battery is still going like it's brand new. I still get the full life out of it and it still charges in the same amount of time as it always did, whether it's in use or turned off. There has been no reduction in the battery's effectiveness whatsoever. I tend to charge my DS 4-5 times a week (yes, I use it that much) and I've had it for quite a while. I got it in Japan when the Lites first came out, and it's still going strong.
Don't worry about waiting for that red light. Only NiCd batteries suffer from the "memory effect".