Manually means, replacing the old markup with the new markup. Brian has info on this already – http://www.briangardner.com/code/genesis-html5-markup/
And also replacing the old hooks with the new hooks. Info on that can be found here – http://www.briangardner.com/code/genesis-html5-loop-hooks/
There’s not really a step by step needed if you follow those 2 links plus the links from the other page listing all of the resources.
Basically just go through your css and replace the old code with the new by doing a “Find/Replace” function. This can be done with any css editor. Same thing for your other theme files. If you don’t see the code from the links above in your files, then don’t worry about it. You only need to replace what you see. Depending on which OS you have, you can do a search for a free html/css/php editor and it will make it much faster to do. Just make sure and save a copy of your current theme in case you make a mistake.