Before you do anything, create a backup of your database and your files.
Considering you are using MSSQL, you don't have worry about your database and the pages are contained within the database.
If you made any changes to your web.config, make a note of the changes and merge them into the new web.config.
After merging your web.config changes with the news web.config, you can safely upload all of the files to your host. You can skip copying the \data\skins directory and then only copy them later if you want them. I suggest using FileZilla as it provides an easy to use process for re-queuing files that didn't upload successfully.
Once the files are uploaded, browse to /Setup/default.aspx in your web browser.