Migrate from debian stretch package install to manual installation

I’m currently running an owncloud 10.4.1 on Debian Stretch and have installed it through the owncloud apt sources.
Those sources however take some time to get the latest update and I’ve read that its more reliable to install owncloud manually so I’d like to migrate the current installation to manual (Unless someone has a reason why thats not a good idea), and would like to know if there are any instructions/documentation to do so and/or if its as simple as backing up the current DB, data and config files and removing the current installation from apt ?

Thanks for any help!