For anything that is in your .bib file already it's simple to group those citations using biblatex. See Sectioning bibliography by type of referred item for a basic example. Since you've manually entered the unpublished sources, and the format you want them in isn't terribly conducive to a .bib solution, I suggest organizing them in a CSV file and using datatool to print them.
The following document as proof of concept does what you want. First, the CSV file. It has the following column structure:
ArchiveName ArchiveAbbrev SourceName SourcePrefix SourceNumber
So a single row corresponds to an individual item:
"Archivo di Stato di Firenze", "ASFi", "Mediceo del Principato", "Filze", "810"
In the sample document I've used simple sectioning to format the headings, but you could do this any way you like really. The code is quite simple: I read through the file and produce headings as needed, otherwise I output a comma and a source number. There is no sorting done of the entries, as this is easy to do in Excel or OpenOffice.
\begin{filecontents}{manuscripts.csv}
"ArchiveName","ArchiveAbbrev","SourceName","SourcePrefix","SourceNumber"
"Archivo di Stato di Firenze","ASFi","Mediceo del Principato","Filze",810
"Archivo di Stato di Firenze","ASFi","Mediceo del Principato","Filze",4323
"Archivo di Stato di Firenze","ASFi","Miscellanea Medicea","Filze",2634
"Archivo di Stato di Firenze","ASFi","Strozzi","Filze",480
"Archivo di Stato di Mantova","ASMn","Archivio Gonzaga",,"b1117"
"Archivo di Stato di Mantova","ASMn","Archivio Gonzaga",,"b1140"
"Archivo di Stato di Mantova","ASMn","Archivio Gonzaga",,"b1920"
\end{filecontents}
\documentclass{article}
\setcounter{secnumdepth}{0}
\usepackage{datatool}
\DTLloadrawdb{manuscripts}{manuscripts.csv}
\def\lastsource{}
\def\lastarch{}
\begin{document}
\DTLforeach{manuscripts}{\archive=ArchiveName,\archabbrev=ArchiveAbbrev,\sourcename=SourceName,\sourceprefix=SourcePrefix,\sourcenum=SourceNumber}{%
\DTLifstringeq{\archive}{\lastarch}
{\DTLifstringeq{\sourcename}{\lastsource}
{, \sourcenum}%
{\let\lastsource\sourcename
\subsection{\sourcename}
\DTLifnullorempty{\sourceprefix}{}{\sourceprefix~}\sourcenum}}
{\let\lastarch\archive
\let\lastsource\sourcename
\section{\archive\DTLifnullorempty{\archabbrev}{}{ (\archabbrev)}}
\subsection{\sourcename}
\DTLifnullorempty{\sourceprefix}{}{\sourceprefix~}\sourcenum}%
}
\end{document}

.bibfile and you're usingbiblatex-chicagofor them, but none of your manuscript sources are currently in a.bibfile at all? And the final output you want will be your regular bibliography and then a "manuscript" bibliography organized in the way you say? – Alan Munn Jan 16 '16 at 15:20.bibfile with the exception of manuscript documents. A typical "manual" citation would look like:\footnote{ASFi MP 4463 f.43r-v}– Clemclem Jan 16 '16 at 16:03.bibfile with the proper entries. Would you be able to show what you have so far as well as a "mock-up" of what you would like to get? – moewe Jan 17 '16 at 17:12primarysource.bibdoes not exist? Published manuscripts (whatever these are) are also only cited that way in footnotes? – cfr Jan 19 '16 at 00:21@manuscript, and 'bibliography driver' for it. This would be the best way to integrate it into the other parts of the bibliography. – jon Jan 19 '16 at 05:22biblatexsolutions. – moewe Jan 19 '16 at 07:15