"If you are going to print hundreds or thousands"...

If you need 500 copies of the same CD you get the CDs pressed and the pressing plant does all the printing: tray cards, on body, booklet. And definitely use a proper DTP program to do the layout for the reasons Geoff explained in more detail than I did, and because the pressing plant with want the artwork professional grade PDFs.

I don't think that's what the OP wanted though, I think it was for a handful to be home-made.

(I learned a hell of a lot of new stuff about printing by doing this, like why and how to export CMYK instead of RGB, and to set black text in overprint mode but other coloured text in knockout, and that Adobe reader is the only viewer that will show overprint properly, and how to use Scribus...)