In order to use something else than the default HTTP challenge, you can set the variable TRAEFIK_CUSTOM_ACME_RESOLVER to the provider you want to use (list of provider codes is here) (e.g. cloudflare) in your .env.
Then, configure the required environment variables (listed in the above referenced list) in .env.custom file.
For example, with Cloudflare you should at least set both CF_API_EMAIL and CF_API_KEY.
Then, the usual:
./run-seedbox.sh