When you 1st have itunes and ipod connected it is set as defualt. This mean when you add a new track on your ipod via itunes it backs it up on your computer as well in itunes folder. Also as you put it from cd if cd is not in drive when you next connect ipod thats why you get explanation mark next to all.
The best set if you go to preferences is to make it manual and make it so it does not back anything up. By having it manual means you can upload from externals, cds, and not need to have it in next time you upload. I have all my songs on my external. If I download a new album to my computer, I just drag it onto ipod via itunes. After its done this I just backit up myself onto external and then delete it from hard drive.
Hope that helps.