There is no single, straightforward way to cite materials from manuscript collections.
In general, your citation should include the title and date of the item, the name of the collection, and where that collection is located. Numerous examples may be viewed in CMoS 14.127 and 14.128.
In a footnote, begin the citation with the specific item.
F: Afrin nasal spray bottle, B0171, Leonard Bernstein Collection, William and Gayle Cook Music Library, Indiana University, https://archives.iu.edu/catalog/VAD8042aspace_VAD8042-02095.
In a bibliography, begin the citation with the name of the collection, or the author/composer of the items in the collection.
B: Leonard Bernstein Collection. William and Gayle Cook Music Library, Indiana University.