I don't think so, you have to boot into Gateway classic mode to play cartridges in emunand.
Regular Gateway emunand only loads from the red cart alone, so regular carts won't read.
If I remember correctly, you hold L while booting Gateway to access the Gateway menu, then choose classic mode.
You have to put the Gateway red card into the 3DS for it to boot emunand even for classic mode. Then take the cart out and put in a real game cart.
HOWEVER, you can use Rxtools to boot into emunand and play carts with no special setup.