In the file manager those are basically just shortcuts and that is why it asks for a name if you go to add one. This part of Kodi is seperate from the rest of Kodi. As for your library, which is the part you set in Videos, they ask for a name as you are setting up sources. You can have more than one file path in a source. What they are named doesn’t matter.
That being said you should understand exactly what you want to do. If you setup new sources for you library and leave the old ones then all your content will be duplicated. If you change your current shares to the local paths your content will be duplicated. If you want to make it so your library uses the system mounts instead you must either dump your existing library and scrape new or alternatively leave your sources exactly as they were and use path substitution to seamlessly redirect the paths in the background…