updating to 2.9

Hi,
I downloaded 2.9 on to my hard disc and now I assume I have to get it uploaded to my cpanel. But 2.9 consists of so many files. I am going to up load each of those one at a time? Way too much work so I suspect this is the wrong approach.
I opened up the directions and they don’t make sense. How would I know which files on WordPress have been modified? I am using DIYthesis so I suspect I have modified nothing.