It depends on the browser, chrome for example uses an xml or a sqllite file, so I'm aware of no way to merge these without writing something that can read that file. For internet explore and I think edge still uses the favorites folder in the user profile, so you just need to push the file to that folder.
Assuming you are referring to IE Favorites, you can go to
User Environment Manager > Files and Folders > Create > Give a name and description > Select the Create button and Wndows will open with multiple folders > Select Favorites > Stores your favorites shortcuts and click Save
Will I be able to merge 5 new favorites into my users favorites, that is already filled with their favorites, without overwriting their favorites/bookmarks..??
For IE favorites are just files, if you overwrite any, they would be the same thing they had anyway.
I believe it will merge what does not already exists and skip the ones that do exist because two shortcuts with the same name can not co-exists. I remember that was the case when I set my environment up. Test it and see.