I've been in the midst of a daily back-and-forth email discussion with the app-schema developers on the GeoServer-Users mailing list. Reading through the conversation may be helpful, as they've already resolved a number of issues I've had. Here's a link to the thread:

http://www.nabble.com/Geoserver-2.0-availability---included-app-schema-capabilities-td24624783.html

I'm almost done building a complete mapping file that will output GeoSciML MappedFeatures from polygon features in a database that follows the NCGMP09 schema. This schema, developed as part of the USGS National Cooperative Geologic Mapping Program, is a proposed standard database schema for the publication of single digital geologic map. An ESRI Personal Geodatabase implementation of the NCGMP09 schema is available on the website linked above.

It works! Once you get the app-schema extension installed and the tutorial data in place, it works just fine. Make sure that in your GetFeature requests you specify the outputFormat as GML3, as it won't work at all in GML2 (which GeoServer defaults to if no outputFormat is specified).

Also, be aware that the app-schema extension is only supported at WFS version 1.1.0.

Now I can move on to beginning to map my data into GeoSciML features. I'll write some more walkthrough as I put it together.