Moving files around in LR5

I have imported everything from my external hard drive in LR5 so I can access all of my photos and move them around to organize them.
I started the organization process and moved files around in different folders via LR5 and I am happy with that.
I then noticed when I looked at the folders that should now be empty on my hard drive (viewing via Finder) the photos that I have moved in LR5 are still where they originally were when I look at the hard drive in Finder.
I want the organization that I did in LR5 to be exactly the same when I look at the files and folders on said hard drive in Finder.
I hope this makes sense and I hope someone out there is able to help me.
Thanks in advance!

I decided to go the long way and move everything where I wanted it to be.  I moved everything around in Bridge, I then synchronized the folder to reflect how it should.  So far so good!
Thank you all for your help and interest, I really appreciate everything!
I do have one more question now, I will also start a new thread to see what else I can get, but again thank you!
I have syncroniced the folder after making the changes, and due to the problem I was having last time I did it again just to double check.  It said there were over2k photos missing so I clicked sync, let it do its thing.  And just to tripple check I ran it again and it is saying the same thing, missing over 2k photos.  What does this mean?

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