Upgrading Etherpad Lite if you installed with Git
/etc/init.d/etherpad-lite stop git pull /etc/init.d/etherpad-lite start
If you installed from the tar ball then grab the latest tar and extract it over your current install.
Make sure you always back up your dirty.db if you use that.
As far as database migrations we are hoping that the current schema wont need any modifications, if so we will try to handle this with upgrade scripts that will run automatically.