Hi Donnie,
FPP is used for multiple batch processes in FS-PM. You can find a detailed description in Chapter 4.6.1 "Description of Batch Runs Implemented in FPP" in the FS-PM Operations Guide.
To 1.: I don't know the Logistics solution. Main use case of FPP is for updating the policies on a regular basis but there are also BI extraction runs for FS-PM built on FPP.
To 2.: I'd say use automatic unless you have a good reason to go manual.
To 3.: You're on the right track! There is also information on this in the Operations Guide including a sample program. The 5.3 delivery also includes some programs for this. Check out /PM0/FPP_EXT_*.
Best regards,
Michael