You can use the
chapterbib package for that purpose.
This is how I normally use it.
I create a main file, let's say:
This is the file where I save my chapters
This is my first appendix
and this is the second
biblio-chap1.bib is the overall bibliography and
author2 citations come from there.
biblio-app1.bib is related to the first appendix and
app1 citation come from there, while
biblio-app2.bib is related to the second appendix and
app2 citation come from there.
To get a fully compiled document, run
Having a look at its documentation will anyway let you know how to adjust it for your needs.