While some of the maps reside in the Map Case (the oversized ones), most of the collection is shelved upstairs on the front wall, closest to the West Virginia Archive (Rm 310). It is, however, a good option to check the library catalog for the item you are searching for and its placement in the building.
All government documents are filed by issuing agency(Education, Interior, Defense, Homeland Security, Census) combined with an internal numbering system. This classification system is called SuDoc.
Exploring maps U.S. Department of the Interior, U.S. Geological Survey.
Government Documents (paper) 3rd floor Range 31
For explanation of the SuDoc system, see Michigan State's webpage.