Actually Charles is going down the right path here.To create a BO and then map it all you have to do is this:
- Create or open a VS project or solution
- Create a BO by right clicking the project then clicking Add item then select SF Business Object
- At this point if you open the BO Mapper, you will be able to see you project and get to the Configure Project after selecting the appropriate project from the tree view on the left. (probably the step you are missing)