Windows MP is bad iTunes is worse!. The reason it will not sync, or syncing can cause problems, is down to what I said about playlists. Win MP playlists are in the .WMP format and your player cannot read them. It does not support iTunes.
Reading throught the instructions it looks as though your mp3 player plays.... mp3s, so all your music should be in mp3 format before you put it on the player. The FreeRip software mentioned in the instructions is pretty good. I have used, it along with CDex and EAC, and it does the job.
http://www.freerip.com/Same with video. It only plays .AMV files so they have to be converted first.
As for the stuff you already have on there, and some of it is not readable by the player, I would start again. The player should have some software to allow you to format the public part of memory. Doing that should clear all user added files and leave the player in out-of-the box state.
The player can hold about 4000 tracks. That's not bad! However, if you are going to be putting that many files on from your computer you will probably need to set up a files system on your computer dedicated to it and to music, but using Windows (My Computer/Explorer) instead of Windows MP or iTunes.
Something like this on your C:\ drive:
Di's Music mp3(root folder)
\Soul
\Punk
\Classical (music styles folders)
\Four Tops
\Supremes
\Temptations (groups/bands/singers folders in the styles folders)
\Don't walk away Renee
\Baby I need your lovin' (individual tracks)
If you wanted to find Don't walk away Renee it would be in:
C:\Di's Music mp3\Soul\Four Tops\Don't walk away Renee
Using Windows you can copy and paste these folders or individual files to the mp3 player.