Q: iTunes on OS X vs Microsoft Windows 8.1

iTunes: 12.0.1.26

I recently completely switched to a Mac from a PC.  I was told by an Apple store 'genius' that I could simply copy my music library from my old pc to my new MBP (from the copy I made of my iTunes library on my old pc).  Ever since I did that, my music library is a mess of duplicate files and duplicate folders and a mixture of .mp3 files along with m4p formats.  

System details:

MBP w/ 13” retina display

2.8 GHz Intel Core i5

8 GB RAM

O/S: OSX 10.9.5 Mavericks

In addition to the MBP I have the following

(running iOS 8.1)

2nd Gen iPad (AT&T +  Wireless 64GB)

6th Gen iPod Touch 32 GB

iPhone 5s 

Any insight anyone might have would be so appreciated!!