<<Also, I know DVDs hold way more than CDs, but if by chance I have to use these to reinstall all my stuff, am I going to lose quality or totally lose data?? >>
Nope - they will be just fine
>>Isn't each archive supposed to take only what hasn't already been archived?<<
You have to mark each file as archived for it to be excluded - you can do that by selecting a bunch of files or just one - right click and choose Mark as Archived - then they will be ignored next time you go to archive