99 per cent of what you want to do is answered in this question. Use the sourcemapping technique at the end of that answer to add suitable keywords to your files. Let's suppose you have then "cata" as one keyword (mapped to your files 1.bib and 2.bib, and "catb" as another keyword (mapped automatically to your file 3.bib
The only remaining problem you have then is the file where you want some assigned to one category, and some to another. With that file, assign manually to the keyword field to "cata, " and also allow biber to add its own extra keyword catb.
You now have three categories:
Entries in two files with keywords set only to "cata".
Entries in two files with keywords set to "catb".
Some entries in one of those files with keywords set to BOTH "cata" (manually) and "catb" (automatically).
Now all you do is filter for keyword=cata in your first bibliography, and for keyword=catb, notkeyword=cata in your second. The first picks up both the automatically encoded file and the manually added one, the second picks up all the automatically encoded files but then excludes the one you manually assigned to the first category.
Only trick is you need to put a comma after the manually assigned keyword.
\documentclass{article}
\usepackage{filecontents}
\begin{filecontents}{test1.bib}
@book{book1,
author = "Anonymous, Author",
title = "First Bibliography: Category 1",
date = {2000},
}
\end{filecontents}
\begin{filecontents}{test2.bib}
@book{book2,
author = "Writer, William",
title = "Second Bibliography: Category 2",
date = {2010},
}
\end{filecontents}
\begin{filecontents}{test3.bib}
@book{book3,
author = "Scribbler, Steven",
title = "First Bibliography Again: Category A and B",
date = {1899},
keywords = {cata,},
}
@book{book4,
author = "Poetaster, Peter",
title = "Second Bibliography Again: Category B",
date = {1767},
}
\end{filecontents}
\usepackage{biblatex}
\DeclareSourcemap{
\maps[datatype=bibtex,overwrite] {
\map{
\perdatasource{test1.bib}
\step[fieldset=KEYWORDS, fieldvalue=cata, append]
}
\map{
\perdatasource{test2.bib}
\step[fieldset=KEYWORDS, fieldvalue=catb, append]
}
\map{
\perdatasource{test3.bib}
\step[fieldset=KEYWORDS, fieldvalue=catb, append]
}
}
}
\addbibresource{test1.bib}
\addbibresource{test2.bib}
\addbibresource{test3.bib}
\begin{document}
\nocite{*}
\printbibliography[keyword=cata]
\printbibliography[keyword=catb, notkeyword=cata]
\end{document}

perdatasourceoption, and create keywords for all entries in each.bibfile. Then print by keywords. ... (Edit) Hmm, actually, this is a 'related' question already. – jon Apr 04 '17 at 16:243.bib, but it's hard to say what to do given the information provided so far. – jon Apr 04 '17 at 17:02refsegmentorrefsectionand then print bibliographies for particular bits of the document. – cfr Apr 05 '17 at 00:35