F-Droid will want to handle Apps that you have already installed that are also available on F-Droid (under the same package name).
Sometimes that will fail because of different signatures. In that case simply uninstall the installed version and install from F-Droid.
If you have another App manager installed choose which one you’ll want to use to update each app, by telling the other one to ignore updates from that app. In general I’d advise you to install apps from F-Droid. If updates are more important to you than freedom then you might want to update some apps from another source (I recommend Yalp, which is available on F-Droid), because F-Droid doesn’t update some apps where more recent versions are not 100% floss anymore.
Or in short:
Everything will be fine. Just go on. And if you run into an issue ask us again.