please see my response on your previous post with the same question. If you read the documentation I already pointed you to it has the answers to your questions.
When you upload the new version it has upgrade scripts, after uploading visit /Setup/Default.aspx to run the upgrade scripts and other upgrade steps. You need to upload all the files to upgrade, sql scripts are below the /Setup folder
Nothing about the upgrade will touch your existing skin, but you will need to make changes to update your custom skin as documented in the important skin changes article.