OSX 10.8.2 with the Server.app installed.
Wiki server running.
where do these files live? *so that I can customize the CSS as well as back everything up.)
What databases so I need to backup and what is the best way to do this?
Try looking under /Library/Server or /Library/Server/Wiki/FileData
(in the Finder, type Shift-command-g then paste in the above path)
This may help with the DB backup: http://support.apple.com/kb/HT5585
This will backup the PostgreSQL Database to the file /tmp/collab.pgdump
sudo ./pg_dump -h "/Library/Server/PostgreSQL For Server Services/Socket" --format=c --compress=9 --blobs --username=collab --file=/tmp/collab.pgdump collab