You don't need to use Sheboygan at all.
To start a site from scratch:
In the site explorer on the left hand site create a folder with your site title. Then within that folder add a few more (to keep everything organised) - Data, Layers, Maps, Layouts.
When you load data or connect to a data source, keep the load procedure and data layers in the Data folder, and the layer defintions in the Layers folder, create map layout and web layouts in their folders too. There are a heap of settings/toolbars that are default so it's pretty straight forward and you can customise layouts from there.
To publish the map, you need to save php files on the server in MapGuideEnterprise2009\WebServerExtensions\www (our basic layouts are still sitting in the 'sample' folder) - I think that originally we saved the php from Sheboygan and edited the title and link to the web layout to fit your site.
Good luck!!