Basically you run the diskwriter program (as admin or it will error out). Choose your microSD card on launch. Format the microSD (File > Format). Once that's done, click Options and Change Template. Choose the template txt file downloaded form the sky3ds website.
Choose File > Write to put games on the SD. That's pretty much it.
The template file dictates some configuration settings for the card. However, if the game you want isn't in the template file, you can't play it.
I'm running in to that now. Last 8 games weren't in the template file so... I'm SOL...