Use MT-card's Launcher.dat.
Anyway, it is great that this is possible now. I had been looking for this, but I didn't have enough knowledge on how the 3ds' internals work, so because I'm an impatient person, I bought a flash card.
I nearly did, too. Luckily I spent all my money on Majora's Mask and stuff. Now I have to get this darn CFW to work then I'm set! Unfortunately I don't think it is working out for me, so I might have to retry the CFW installation, since it keeps rebooting the 3ds when I try loading it.