UPDATE: I have figured out the solution, and I will post it here for everyone else to figure out too!
Prerequisite: This for people who have used the Batch CIA 3DS Decryptor and received a .CCI file instead of a .CIA file. This means that your ROM has to already have been decrypted. Also your 3DS must be jailbroken.
Step 1: Simply rename your .CCI file to a .3DS file. Windows will warn you that renaming the file could render it unusable. Just press OK.
Step 2: Insert your 3DS's SD card into your PC.
Step 3: Take your decrypted CCI file and put it into your 3DS's SD card. More specifically, put it into "gm9", then put it into "in".
Step 4: Remove your 3DS's SD card from your PC and insert it into your 3DS.
Step 5: Launch GodMode9. (This is done by holding "Start" while pushing the "Power" button.)
Step 6: Once there, push the "Home" button to bring up the action menu.
Step 7: Use the D-Pad to navigate to "Scripts..." and push "A" to select it.
Step 8: Select "GM9Megascript" by pushing "A".
Step 9: Navigate to "Miscellaneous" and push "A" to select it.
Step 10: Navigate to ".3ds to .cia Converter" and push "A" to select it.
Step 11: If everything has gone right, you should see your .3DS ROM there. Simply press "A" to let the converter convert your file.
Step 12: After your file is converted, just exit out of GodMode9 by powering down the system, power it back on again, and now you're ready to install it with FBI just like a normal .CIA ROM!