I used their docker container in manual mode and the whole process was a great e...

I used their docker container in manual mode and the whole process was a great experience. No need to stop the main server. The steps were:

    1. Run the container without ports in manual mode
    2. Use the GUI to enter account data and URLs for the SAN certificate
    3. Let the client print out the challenges
    4. Copy the challenges to the webroots using the provided command
    5. Press ENTER and wait a few seconds. Certs and Keys are ready to be linked from the webserver.

Everything went as expected and I am a happy user of letsencrypt.

[1] https://letsencrypt.readthedocs.org/en/latest/using.html#run...