The patch can and will remove and overwrite some files and directories (except for UserData, that folder is always safe).
(Optional) Backup any important files in your game directory like private mods.Freely available R18 patches are included, you don't have to install them manually (but doing so won't hurt anything). You don't have to install all of them, you can pick only some DLCs or not install any DLCs at all. Install the game (if you already have it installed, you don't have to reinstall it in most cases).For more detailed info check the GitHub page of your patch.
This is a general overview of the installation process.