Well, if you got something like the 3rd Earth accessory pack, and it includes screen protectors+case+ other junk, or a pack with any set of screen protectors, then it should have differentiated sizes.
What I mean is basically this: what you're supplied is 2 screen protectors, one larger than the other. The larger one goes on the top screen as there is no outerborder thing, and the smaller goes onto the touchscreen.
The DS's touchscreen is pressure-based, not static-based (such as your laptop touchpad, iPod clickwheel, iPhone etc) so a screen protector can go onto it that isn't made for a specific purpose.
Just a note, 3rd Earth uses photo-film as a screen protector, which in reality is not very good(and it shows that they're cheapos). My touchscreen one is ruined because I didn't notice their size and tried applying it to the top >.>(about a year ago tbh) and also it wore down from masses of use. I use a 3rd Party non-ds stylus which are a fair bit better.
I don't know much about the Hori Screen Protectors, but apparently they're the best.