need help with iTunes 12 and windows.

Hey all, I am having trouble with i
Tunes and windows. Big surprise, right? I set it up so my iTunes library is on my external drive and everything synchs to it. Here’s the problem. When I go to add other folders to the library the only folder I see on the external drive through iTunes is the iTunes folder. There are no other folders on the external drive according to iTunes. This is not the case. If I open the folder using windows explorer, all my folders are there. What is going on? Is iTunes just not going to work now and I have to add things in file by file or is this something that can be fixed? Thanks in advance.