You can edit the footer in the layout.master file of your skin. Perhaps I will add a site setting for company name when I get time to make this easier.
Yep we can always use more/better documentation.
Skinning and design is limited only by html and css and graphics skills. Colors and fonts, images and placement of images is all css its not a feature of mojoPortal.
There already is a place for the google maps key in siteSettings under the API Keys tab, though its also possible to set it in web.config and this will trump the sitesetting.
Users can specify meta keywords and descriptions. If you need custom meta tags that are global you can put them in layout.master of the skin. There is actually a secret setting that is hidden for additional meta on pages. Its hidden because its a free form text field and its easy for users who don't know what its for to put something there will break the site or make it invalid markup. If you want to use it you can make it visible by this setting in Web.config:
<add key="ShowAdditionalMeta" value="false" />
The AddThis bookmark button is also enabled from siteSettings by entering your addthis.com username.
Ecommerce is a fledgling evolving feature in its early stage of development. Yes ecommerce configuration can be tricky even for me.
Hope it helps,