Why Does Itunes Store Songs In Multiple Places...

Okay, I've got a question about why on my laptop Itunes stores songs in places other than where I'd like to store them. I'm using a PC with Windows 10, running Itunes12.4.1.6. I had cause to get into the Windows Explorer and Itunes as I had a really stubborn song that wouldn't take the edits I was making to its tag, it would be with its album on my laptop but when I tried to put it over to my phone - an Android - it refused to join the album. It's weird because it's attached to its album in the laptop but not in the phone and it refuses to do so.

But I digress. I've got an external hard drive with Itunes installed on it called the F Drive. It's got a big tree of folders with all my artists, each with a subfolder for each album containing each song for that album. However I also noticed that my C Drive on the laptop itself has some Itunes files and when I looked at those I found a group of songs, not mean maybe a dozen. When I deleted them off the C Drive suddenly Itunes couldn't find those songs anymore. I pointed Itunes to where those songs were on the F Drive and it put a copy on the C Drive again without me knowing it until I went and looked.

So my question is why does Itunes put only select songs in more than one spot? I mean I've got a huge hard drive so it's not like I'm wanting for space, but I am big on organization. I'd like all of them in one spot not two. How can I get them all into one spot that Itunes will recognize and play out of without making itself a copy of select songs?