What OS and how did you install each? I know there was some discussion awhile back on how to do a double installation but I didn’t follow it since I only do the latest release so I can refer to it to help answer questions.
(You will not alter v6.0 or v6.99 configs by running v5 uninstaller. Also, I am windows user, don’t know about linux)
About backups just in case:
If you are using only v6+ already and there is no preferences to be imported from v5 instalation, there is nothing to keep from %appdata%\kicad. User settings of v5 is saved in the root of that folder as a “flat hierarchy (a mess)”. v6+ has appropriatelly called subfolders (v6 or v6.99) there, so keep only theese subfolders.
KiCad 5.1 didn’t version the settings. All files which are directly under %appdata%/ belong to v5. At some point in the development process v5.99 started to version the settings, and each major version (5.99, 6.x, 7.x etc.) will have their own subfolder there and all their respective files are kept under those folders.