Your comments

The command is "pure-pw list".
BTW: What operating system are you using?
please execute the command "pure-pw list" and show me its output. It looks like the user is existing.
Do you have a colon or any other special character in one of your ftp user passwords?

And some more thing: What does the last line "they: option requires an argument" mean?
Hm, my section is showing the process uptime right next to its name. You could try pressing the restart button on top of the supervisor section. For reference, this is how it looks like in my panel:

Yes, i corrected it on github. What is shown on the supervisor section?
Ah, I forgot to mention that you have to restart your websites in the website overview.
You can also look under the "supervisor" section in the left sidebar if your added process is listed as "running".
At first, there is a typo in my script above. Please use the script i have published on github for you:

After creating and modifying the script, you have to save (i have saved mine as /usr/local/bin/scripts/
The following screenshot may show it better:

Please feel free to make further comments if anything is unclear. :)
My guess: Add a website, but don't add a corresponding domain. Unter the ports tab add your IP with port 80.
By default, nginx will now link all undefined domains and/or ip-addresses to the defined website.
Only installing the packages won't overwrite your config. But activating the components in Ajenti will overwrite the configs of the selected package.

For more information about what configs get overwritten, see my search on github.
(The result list has not to be complete..)
Never mind, I found a solution: Create the following script and add it under "processes" in the existing website.
The users are input in format username:password:homepath

SET_USERS="usernameone:password:/path/to/web/folder usernametwo:password:/path/to/second/folder"

IFS=' ' read -a USERS <<< "${SET_USERS}"

for SET_USER in ${USERS[@]}; do
IFS=':' read -a USER <<< "${SET_USER}"
(echo $PASS; echo $PASS) | pure-pw useradd $NAM -u www-data -g www-data -d $DIR
pure-pw mkdb

sleep 1;

One more thing: We are using the ajenti-v-ftp-pureftpd plugin..