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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.
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