According to the Chicago Manual of Style, 15th Edition there is no agreement on the order of elements in archival and manuscript collection citations (17.222). So, while there is considerable freedom in archival citation forms, the author must order the citation elements consistently.
Both are abbreviations for "Manuscript."
Note that the first two bullets may be combined in the title of the collection. If that is the case, simply use the collection's title.
James Newman Clark Collection, 1867-1972. UHC249. Special Collections & Archives. McIntyre Library. University of Wisconsin--Eau Claire. Eau Claire, WI.
University of Wisconsin--Eau Claire. Grambling State University Exchange Program Records, 1970-1980. AS182. Special Collections & Archives. McIntyre Library. University of Wisconsin--Eau Claire. Eau Claire, WI.
Uniroyal, Inc. Eau Claire Plant Records, 1917-1990. Eau Claire Mss CB. Wisconsin Historical Society. Records housed in Special Collections & Archives, McIntyre Library, University of Wisconsin – Eau Claire. Eau Claire, WI.
James Sibree Anderson Papers, 1829-1926. Green Bay Mss 133. Wisconsin Historical Society. Housed in the University Archives and Special Collections, Coffrin Library, University of Wisconsin - Green Bay. Green Bay, WI.