How to use "PDF per directory" mode
This is Sample6.bat contents:
Bmp2PDFPilot.exe /A /D /R "Sample files\*.bmp" /O "Sample PDF files\"
Files list to convert:
All BMP files from directory "Sample files" and it subdirectories
Used required switches:
/O - required switch. Here it tells program create PDF files in "Sample PDF files" directory
Used not required switches:
/A - auto open 
/R - search for files recursively
/D - "PDF per directory" mode
Program create PDF files  in directory "Sample PDF files"
from bmp images located in directory "Sample files" and all subdirectories.
PDF files will be named as directories of BMP files.
All BMP files from the same directory will be added to same PDF file
If output directory does not exist, it will be created
When converting process is complete,PDF file "Sample6.pdf" will be opened.