Trouble synching ipod with itunes

Laptop had a virus which ate its way through most things including itunes (everything was gone). PC World have fixed it but after downloading itunes again and synching in my ipod, the only songs/albums that have been synched have been those purchased from the itunes store itself. Songs purchased via a CD or downloaded from Amazon have not been synched back in. Is there any way of getting itunes to take these songs back on board as it is a bit off it only accepts songs purchased from its own store only.

Many thanks in advance