The script install is really just to save keystrokes. It is nothing more then appdaemon installed in a virtualenv. After a look at your link, I think for hass-apps to work you need to install it manually to the already created appdaemon virtualenv
iocage console homeassistant
su - hass
source /srv/appdaemon/bin/activate
pip3 install --upgrade hass-apps
deactivate && exit
After those steps you should be able to configure hass-apps. I assume your using my example config files? If not then you would need to create your own appdaemon configuration before it will run
Real quick here, The python_packages in your link is for appdaemon in the hass io ecosystem. You are not using hassio if you have followed this guide or used my script. Your install is just a plain virtualenv.
For the apps.yaml I actually just realized I never added one. Again (assume you used my config) you can create your own with this hello_world app from the appdaemon docs.
EDIT I just added the appdaemon test app to my example files
I used /home/hass/appdaemon/apps for apps. I set that location in /home/hass/appdaemon/conf/appdaemon.yaml and you can look there to see and/or change anything.