Synching iTunes with iPod classic

Hi,

My iTunes was a mess having transferred all the files onto an external HD. I have spent ages tidying up all the files, deleting multiple instances etc and now it's good to go in terms of synching up with my old iPod classic.

I am worried that when I synch the iTunes will actually update to match the the iPod? Is this the case or do I need to change some setting to insure the changes on iTunes are 'pushed' to the iPod? Really do not want to have go through all the housekeeping I've done on this again. Would appreciate any responses on this. Thanks