Two other things:
First, although you store your games on your slot-1 card, you copy them over to the 3-in-1 to play them (using a program on the DS). This takes, like, 30 seconds, although a copied game stays in the 3-in-1 until you overwrite it (so you could, in theory, delete it from the slot-1 card if you're really low on space. Not that I recommend that.) You can also boot up straight into the game you currently have in your 3-in-1 if you want, which is nice.
Likewise, the 'current' save for the game currently in the 3-in-1 is stored in the 3-in-1 itself; the copying programs will handle copying it back into the slot-1 card when you change games. I recommend backing your savegame back into your slot-1 card every time you stop playing, though.