The FileMaker licenses are for FileMaker PRO 10 (which is the current latest version of FileMaker) and for a multi-user version you will also receive FileMaker Server Advanced.
There is no difference in the FileMaker Pro application that you receive with BusinessMan, it is the complete FileMaker Pro 10 application.
You will receive a license key for each installation of FileMaker Pro and yes, you can use your own homemade FileMaker solutions with the FileMaker Pro application that comes complete with BusinessMan.