First step is create a standard difference pdf presenter. We use the parent folder of the first file to store the result to.
DifferencesPDFPresenter presenter = new DifferencesPDFPresenter(<file1>.getParentFile() );
After them, use the pdf comparer add the presenter and compare then.
new PDFComparer()
.addPresenter( presenter)
.compare( <file1>, <file2> );