You need to already have a Gameboy Color game downloaded from the eshop then follow these steps.
1.Load up the GBC game you already have
2.tap the touch screen and click restart
3.Right as the game starts to restart press the home button
4.Go to the Internet browser
5.Click URL and go to loadcode.projectpokemon.org
6.Wait for the eshop to give you an error and close itself
7.click back on the game and it should load up the rom
MORE INFO
You need this extracted on your 3ds sdcard
http://www.mediafire.com/download/0583oa67e42jyqf/GBCRomSwap.rar
And the game must not go over 1mb.
MORE INFO THE SECOND ATTACK
Make sure code.bin and your rom.gbc of choice is on the root (first folder) of the SD card. Start up your 3DS and go to the web browser. Pick a bookmark and edit the title to code.bin. Edit the link of the bookmark to the site loadcode.projectpokemon.org. After this, clear your history and cookies. Then restart your system.