Upgrading SkyBlueCanvas is simple because all of the files that are editable are contained in a single directory: /skyblue/data/.
When you upgrade to a new version of SkyBlueCanvas, you simply need to make a copy of this directory, install the new version following the instructions on the Installation page, then copy your data file back into /skyblue/data/.
The htaccess rules may have changed in since the last version of SkyBlueCanvas. Be sure to update the file named .htaccess in your SkyBlueCanvas installation.