It's in the readme (afaik), you need to switch you ds off and on (quick), and then go to "Save", and select the DS2Key.sav (if any, if you don't have one you need an 64kb file with nothing in it (I'm not sure if it is 64kb but I'll make sure when I'm home), the file must have the same name as the DS2Key binary except for the extension (DS2Key.nds -> DS2Key.sav, DS2Key.ds.gba -> DS2Key.ds.sav, but I'm pretty sure you use something like DS2Key.sc.nds -> DS2Key.sc.sav). Just put this file in the same directory where the binary is.