You cannot sign a portion of a PDF. Digital signatures, wherever they might have an appearance, always apply to an entire file.
I do not understand what your problem is. It is definitely possible to sign the same PDF several times. That you have, what you call "two documents" in one PDF file is immaterial. It is still one PDF document/file which is signed as a whole.
I have the same problem since I use El Capitan: I need to sign a form twice. First - no problem. Second - This appears when I want to save the file: "The file may be read-only, or another user may have it open. Please save the document with a different name or in a different folder."
The past was easier . Hope somebody has a solution.
I have a different but related problem. Documents issued by a company have to be signed by two directors (section 44 of the Companies Act 2006). This was emphasised by a recent case, Bali v Manaquel Company Limited, County Court at Central London (HHJ Hand QC), 15th April 2016, in which the applicant lost by virtue of a critical document not being signed by two directors.
How do two different people, possibly at two separate locations, sign the same document?