I am not sure - Are you upgrading from V1 to V2, or are you upgrading from an earlier version of V2, to the latest?
v1 -> v2
To upgrade from a V1 gallery, you can keep your images/folders in the "content" folder but nothing else. Delete other folders, and simply upload the v2 files- and folders(except the "content" folder as you wish to keep the one you had).
v2 ->v2 upgrade
To upgrade your V2 gallery with latest release, simply upload all files except the "content" folder. New files will overwrite old ones, and you keep your content with images- and folders.
Not sure what's wrong with
www.susanwattsphotography.com/gallery - Seems to be working fine here, except perhaps one issue: Startpath is set to "content" which doesn't contain any images, so startpage remains blank. You need point startpath to an actual gallery folder or a textpage if you want am opening page.