I was just wondering if there was an easier to upgrade then re-uploading all the files over the files of an older version say 1.4.5.9 to 1.4.6.0 . I usually have to re-edit all the template changes I made every upgrade. Is there an easier way where I don't have to do that. Is there a features like wordpress auto upgrades where I just push a button and it upgrades my zenphoto version without me having to upload and re-edit everything?

There is no WP like upgrade via a button yet. That is on our To Do List but believe me this is by all means not a trivial feature and must be thought out very carefully.

Given the reports of file/folder permission issues that many have on their shared servers here that is likely to kill sites completely. Also the security part of it.

But even if we had such an update function it will never save you from having to update your theme. We always do update our included themes but since we don't know yours you have to do it yourself. We always try to keep changes to necessary minimum but some are sometimes needed to improve the internal structure and make it so called future save.

I'm just using the Zenpage theme with a few modifications like added Facebook buttons and the such.

That does not make any difference. If you replace the theme, you have to re-apply your changes or if you don't you have to ours. No way around. Whatever upgrade we will have it cannot know your changes.