E1 Batch Ship Confirm

We are trying to set up Batch Ship Confirm.  We need to know what the entire process is.  We want to load a text file from an outside source and process the file to do partial shipments on our Sales Orders. 

I have been reading various documents but am really confused by what each program does or doesn't do.  I did get the R47071S to run against the F47071 and F47072 files, but it only updated the status code.  It didn't ship the product, either in whole or partially.

Any help would be appreciated.