To install a custom package, get it from which ever source you like and then configure Apache. Installing with apt-get is recommended as you get automatic security upgrades with it. After this you need to configure Apache for your application. You should consult dockwiki documentation for this, but roughly speaking you will need to create a file /etc/apache2/conf-available/my-docuwiki.conf
and write something like
Alias /docuwiki /path/to/docuwiki/
and run
a2enconf my-docuwiki
This is needed only if the Debian package already does not provide the configuration file. See examples in /etc/apache2/conf-available/
for configuration files provided by FreedomBox. You don’t have worry about PHP configuration or Let’s Encrypt certificates as they are taken care of by FreedomBox. You will then need to proceed and configure docuwiki (such as database etc.). Follow the usual process as you would with Debian. FreedomBox will mostly stay out of the way.