I have a few questions/concerns before I upgrade to 1.3
1)I have customized my css and show files quite a bit - will these be overwritten?
2) I've added lightbox to my site, will this be affected?
3) Where do I find the documentation for upgrading? I think I'm missing something and just want to be sure.
1) The css and show files are in the themes directory, so they should not be affected by the clickable upgrade of the Omeka core, but it is always best to back up your entire existing installation and particularly files you have modified. The zip file for 1.3 includes new default, minimalist, rhythm, and seasons themes. You can replace these with your backed up theme folders or files after installation.
2) Again, I assume lightbox is somewhere in your themes folder, so the same rules apply as for the other theme files.
3) Directions for upgrading are here. http://omeka.org/codex/Upgrading
It is particularly important to back up your database and to disable all plugins.