You could try to get your Applications directory via SSH, upgrade, and then put it back. But i'm not sure that's going to work...
Keeping your sources is much easier, you have to get (via SSH) a few .plist files in the Installer folder on your iPhone. You could then put it back when you upgraded.
Even easier is this: Just upgrade, add the sources you want to
Your Repository; you then have to add only one source to your Installer.