If your intent is to merge two existing music folders, iTunes can do that with relative ease. There are two different but related entities, the iTunes Library and the tune files. Although it is generally preferable for management purposes the tune files do not have to be in the same folder, or even on the same drive to be included in the iTunes Library. The organization of the Library is independent of the organization of files in the various folders.
You will find an easy step-by-step discussion of how to combine or merge two iTunes Libraries and at the same time into a single iTunes Media folder
here. If you would prefer to keep the tunes in multiple folders and/or locations do
NOT check the option to consolidate files.
As to the organization within the Library itself, that can become quite difficult. Everything has to be letter perfect, the artist name, the album name, the album artist, composer,
etc.,
etc. I have found those are not always consistent even in the same downloaded album, which can result in an album appearing multiple times in the Library.