iTunes works by copying files from your computer to your iPod. You can't delete music off the iPod directly.
Depending how you have your iPod set up with iTunes (plug it in and see), it can either copy everything from your iTunes library to iPod (if space allows), or copy some stuff, perhaps with 'autofill' to choose a random selection for your iPod each time.
Or, you can manually control your iPod, and add and remove songs as you like, through the iTunes interface.
All these options are available in iTunes when you plug in your iPod.