Hi,
Web.config and user.config doesn't control which data layer is used, we have different connection strings there for each data layer and each data layer uses its own connection string but that does not control which data layer is used.
Which data layer is used depends on project references from the business layer, we have build profiles that automatically set the correct references then when you rebuild the solution the correct version of the data dlls is used.
See the screen shot in the Packaging and Deployment article.
Hope that helps,
Joe