Akeeba Backup First - Entire site
If you have changed the core files they will be overwritten.
There is a post here somewhere where Fotis reccomends a source code comparison utility for both pc and mac
Check your k2.css and other files in the core against the ones you are fixing to install.
There should be some differences, but there should also be all the edits you made as differences...They will have to be redone.
Overrides and css4k2 will eliminate most of this, and it may, depending on the site be eaiser to do the overrides first, then upgrade...