That’s highly dependent on the environment you’re deploying Caddy in.
Assuming you’re on one of the common flavours of Linux, the simplest way would be to type CLOUDFLARE_EMAIL=myemail@example.com and CLOUDFLARE_API_KEY=123xyz in the shell before running Caddy.
If you plan to use an init system to run Caddy for you, you’ll need to make sure it handles setting the variables - again, depends highly on the system you use.