Applications :: ITunes Music Files Messy - Reorganize Everything All Over Again?

I am a "sort-of" new iTunes user. I used to use it to play music without care of how to use it properly. Since I did not want to carry many CDs around, I copied all the CDs into the HD of my MBP. For simplicity, let's say I named the folder of the first and second CDs to be CD1, CD2. I don't remember how I stored the files. Either by drag and drop to the list when iTunes is launched or by some kind of import function from iTunes. The files in the iTunes folder do not seem to correspond to those shown on the iTunes list. My music files are all over the places. Some in the library folders and some seem to be in the playlist. Some of them seem to be in the unknown artist folder, etc. It is like a mess. As I just bought the IPT, I want to re-organize the files before syncing the music files from my MBP to the IPT. What is the best way to do in this case?