No, when you are playing GBA games you just use the d-pad, the A & B buttons, the L & R buttons, select, and start. It's set up just the same as on a regular GBA or GBA SP.
The stylus and X&Y buttons aren't used for anything on GBA games.
I've been playing some FFTA on my DS and I have to say that I have an easier time holding the DS than the SP. The DS is long and I can spread out my fingers better. On the SP they feel more cramped together. The sound is also better coming from the DS's stereo speakers. Everyone says the games look better too but I haven't compared a GBA game playing on the DS to a GBA game playing on the SP, so I don't know about that yet.
Mostly though I'm playing the mini games on SM64 DS and trying to beat my high scores. It gets addicting. Like in Wanted, my friend got a high score of 29, so I had to beat that. I got up to 41. I was just playing it now and I got up to 63! :woot Sometime later I'm sure I'll beat that!