Okay, so if I have installed lots of other stuff via Aurora & fdroid, but I want to use obtainium to manage my installs is there a way to get it to detect everything & take over that job or is there a lot of manual uninstalling & reinstalling that has to be done?
Fdroid reporsitory often lags with updates. Apps often itself check source (github) for latest update on startup and prompt if available - nothing fishy.
It's recommended that you use fdroid/source packages only. Can try obtainium for updating all apps at once from GitHub if you find F-droid updates slow.
Another rec: do check out the Newpipe x Sponsorblock fork ( https://apt.izzysoft.de/fdroid/index/apk/org.polymorphicshade.newpipe), it'll cut out in-vid adverts or libretube if you'd like a better UX. Izzysoft is an amazing repository for FOSS F-droid Apps.
Aurora is great when you need a google play app. Although you should switch to F-droid version of Amethyst as it doesn't have play services built-in (used for translation and notifications).
Grab the Amethyst GitHub link ( https://github.com/vitorpamplona/amethyst) and throw it into https://github.com/ImranR98/Obtainium and it'll take care of all future updates.
1 more tip, F-droid client can be slow and clunky, try neo store (available on F-droid) for better UX and app discovery.
Discussion
It should work, throw the github url for an app into obtainium and try updating. It should update and keep the settings.
If this fails, I'd say one time obtainium setup would be required. No need to get everything through obtainium (do amethyst as it updates frequently and runs ahead of fdroid a lot).
Much of stuff you'd have installed through aurora would not be open source and if it is you should use fdroid/github versions as they'd lack the Google components. Use aurora for apps that are not available elsewhere, better than sourcing apks on shady websites. Aurora pulls from Google directly so at least they are as published by devs.
Do try neo store/izzysoft repo combo for most of you fdroid installs, it'll take over updating without issues for fdroid installs.