First off, did you buy just an expansion pack (like for the M3 Real, that expansion pack?), or did you buy an actual M3 Lite flashcart?
If expansion pack: Assuming you have the M3 Real, you just run them from the GBA menu in the OS (I think you can do it from the folder browser too, but I don't think I've tried that yet). If not, then I think you have to use GBA Exploader or something similar, because I think it does work with that. Or at least it's similar hardware to the Ewin Expansion Pack.
If actual flashcart: Just boot your DS in slot-2 mode. These carts just work as GBA carts that support booting into NDS mode.