Itunes Showing library different then Ipod Library

So my computer crashed and had to be reset. I have 20k plus songs on my Ipod, with only about 1000 purchased from Itunes. (Most came from Cds i owned). Anyway, when my computer was reset my music library was saved and backed up. When I redownloaded Itunes I added that folder to Itunes and got the 20k songs back into itunes. I then plugged in my Ipod and it recognized it, but it was seperate from the Itunes library if that makes sense. If i tried to sync to the ipod from the itunes library it wouldnt download the few new songs. Its like its different or seperate, almost like the ipods library is different then the Itunes. How do i get it to sync or be one in the same. One thing I noticed is that when i click the device the ipod it shows all my playlists but i cant move songs from itunes in the playlist i can only make a new playlist in itunes under music playlist. Like i said, it seems like it is seperate. The ipod has like 21800 songs and the itunes has 22300 ish. Obviously its the same **** library but being read as seperate. I hope that makes sense. Any help would be awesome. Should i just erase the ipod completely and sync the itunes music library too it or what and how do i do that if theres not another way? Please help. Thank you.