First you must format it into "emunand" mode. To do this you must create another emunand on the SD card you want to use. After that use your emunand tool to "inject" your old emunand.
But now I have to tap on rxtools to get into it. Before when I turned on the 3ds I had to hold L button to get into the homebrew launcher. Is there a way to put it back to the way it was?