Wait for the file to be created and you're set.
After you have filled out the metadata and such and you think you are ready, click 'Project' and then 'Export CIA'. You can mess with the injection method yourself but the 'GBC Virtual Console' is the normal format and used by the GB/GBC games on the store. You'll need to insert the metadata and game icons yourself. Once the screen changes, click 'Project', then 'Load Rom'. Once it is open, you'll want to click 'File' at the top left, hover over 'New', and then click 'Game Boy Color CIA'. Once this is downloaded and installed, open it up. To create a CIA file yourself, the first step is to install a program called 'New Super Ultimate Injector' (NSUI). This is all assuming that your 3ds is modded and you have a CC 2.4 GBC file downloaded.
