SimpleIndex can create PDF files with bookmarks based on the index data captured in your batch.
Going the other way–splitting an existing PDF file based on the bookmark value–is not a built-in feature of SimpleIndex. However there are inexpensive command line utilities that you can integrate with SimpleIndex in order to accomplish this.
For example, the CoolUtils PDFSplitter and A-PDF Split both offer this function starting around $35.
The command line to split the PDF can be integrated into the Pre-Process setting in SimpleIndex, found under the Advanced Settings section of the Configuration Wizard. An example pre-process using PDFSplitter to split based on the second level bookmark values would be:
PDFSplitter.exe “c:\Images\BookmarkFile.pdf” “%CONFIGFILEFOLDER%\Input” -em bookmarks -b 2