The R4i Gold Deluxe or whatever the fuck it's called comes with 2 cards: one which is a DS cart that is only used to install the exploit, and another one for running 3DS ROMs. Once you set up the SD/micro SD according to the instructions in the update you'd download from R4's site, do the following:
- Insert the DS cart in your 3DS
- Launch it and install the exploit by tapping on the file you would've added to the micro SD card inserted into the DS cart Once that's done, you no longer need to use the included DS cart at all, since your girls won't be playing DS games on them.
Once you're done with that, you write the ROM to the micro SD you'll be putting into the OTHER flashcart for 3DS ROMs, and follow the instructions I outlined above. Not to sound like a dick, but you really should read the instructions that R4 includes in the firmware release on their site for that flashcart. It outlines the steps pretty well, with pictures even!