Question Regarding Upgrading

[Tr!p]

I did not have the best of luck upgrading Classifieds. Ended up having to drop the related tables and do a fresh install. I was trying to pin point exactly where I went wrong so I don't make the same mistake with Reviews.
My confusion is here...

upload all the new files except your config files and header footer files etc

It's the header, footer files that is a head scratcher to me. What directory are these located in? And specifically what does "etc" relate to?

[Chuck S]

well if your loading header footers this would depend. I am merely refering to our header footer htm files we provide in our download as some people use them. Thats just a cautionary statement I dont want you overwriting something that you are using.