Ensure you have the latest boot.firm and boot.3dsx from the Luma3DS GitHub . These should sit at the root of your SD card (and thus the root of your zip).
If you are building a custom pack to quickly set up multiple consoles, follow these steps to organize your .zip correctly.
Only download pre-made zips from trusted community members on GBAtemp or official guide sites. Malicious files can brick your console. S_yExclusivezip
Are you trying to for a specific custom firmware version, or are you having trouble running a script from a file you already downloaded?
For the most up-to-date and safest methods, the community-standard resource remains the 3DS Hacks Guide . Ensure you have the latest boot
If you have downloaded a pre-made pack, follow these standard steps: Open the file on your PC.
If the pack included a script, navigate to [0:] SDCARD -> gm9 -> scripts and run the setup script. Only download pre-made zips from trusted community members
Always back up your sysNAND via GodMode9 before running automated scripts from a zip file.