I've got Drupal working on a shared host, and I uploaded some modules from my home system successfully, but I've got the message that there is a security update for my version, and I should update immediately.

I'm not sure how I'm supposed to do that. It seems like the update is an entire new installation. I originally installed it using the hosting company's installer, Fantastico. Should I simply over-write the existing installation with the new files? Or ignore the message? I realize I shouldn't over-write the sites folder, or anything I've modified.

The instructions that come with the download seem to be for a major version upgrade, and are way too much trouble for frequent security updates. Searching Drupal's site shows many other methods, but no indication of anything official. And some were ridiculously error-prone, and not really useful.

I don't have shell access to the hosting site, although I can pay extra to get it if I really need to. Or, maybe I can clone the site on my local Linux system, do the update using a script, then upload the whole thing.

Does anyone have experience with this situation?