In 1992, the Bureau of Canadian Arichivist published a report
entitled "Subject Indexing for Archives: report of the
on Subject Indexing Working Group"  The report examined issues
related to indexing of archives including  multilevel indexing and
made a number of recommendations.  Three of the recommendations
address some of the the questions you asked.  They are:

2.  We recommend that index terms be derived, not from the documents
themselves, but from their secondary representations, that is, the
archival description(s) prepared for them

3.  We recommend that archival indexing, like archival description be
based on hierarchical levels of description and proceed from the
general to the specific.  An item should not be indexed before the
file, series and fonds to which it belongs.

4. We recommend that the specificity of index terms also be tied to
hierarchical levels that is index terms at the series levels should
be more specific than index terms at the fonds level.

The Working Group felt it was important to address the practice of
providing specific index terms to a collection level description.
You might want to read the full report before deciding on how to