in my s9y installation, I made several changes (Wiki notation starting from a specific blog entry, but also some environment variable issues due to a manual installation of ImageMagick in my web server account).
When upgrading to a newer version (what is needed quite often due to s9y's developmental status
), all of my changes (including the template!) is killed anytime and I'm forced to patch it all in again. 
Some changes can't be made automagically, sure. But is there any safe place where to put changes? How can I have my template preserved? Or, can I mark some files as "to be updated manually"?
I use the shell script provided with s9y for upgrading. Maybe I'm just doing it wrong? How do you update conveniently with as few patching as possible afterwards?
I only have ftp access to my host. After I ftp the new version of s9y over, I then ftp my changes. I usually do a diff first to see if there are major changes between the versions tho, just to be on the safe side. As for the templates, I found that the upgrade leaves it alone, as long as your own template aren't named the same as the ones that come with s9y.