Syncing with external hard drive issue

[Moomin]

Hi all, I have a new laptop and for space issues wanted to keep my iTunes library on an external hard drive rather than the laptop's hard drive. I changed the library location in iTunes to the external hard drive and then imported some new stuff, which went into the same folder on the external drive as all my other music.

So far so good...

Since it all seemed to be in the same place (an ignoring the rather obvious clue that it wasn't going to work - that I actually couldn't see the folder contents through iTunes - hindsight is a wonderful thing) I told my iPod to sync. It detected that I had bought songs that weren't in the iTunes library (a bad sign but by than it was too late) so copied all of those but I've basically managed to remove nearly everything from my iPod.

The thing is looking at the tutorial I can't see what I did wrong - all my music is in the same folder on the external hard drive and that's the folder iTunes is told to look at, can anyone help?