Programatically, Java is the language used to implement business logic that would plug into LiveCycle. I believe you can use C# for older versions. However, that information is irrelevant to your problem.
That being said, it's typically not advisable to be modifying PDF files generated by different applications (iText, Adobe LiveCycle, etc.). While both documents may render out as "PDF", they will not be created internally in the same manner. I would advise that it may be easy to add PDF files generated by other applications as attachments, they are not going to be easily handled unless you address each specific document in a custom manner.