That's a very good question! There are all kinds of commentaries in both places. There are mainly two differences.
- The commentaries in the main collection can be checked out. The ones in the reference collection can only be used in the library.
- The second difference is in the way they are organized, or shelved. The commentaries in the Reference Collection are kept in publisher sets, so if you wish to study the book of Joshua you would need to check for a volume on Joshua in each set of commentaries.
- Upstairs in the main collection the commentaries tend to be shelved mostly by the book of the Bible and are organized in the same way they occur in the Bible. Therefore, you'll walk through the B's and see on the spines of books that many are about the book of Genesis, then you'll begin to see books about Exodus, and so on.
- If you still have questions - ask a librarian or a research T.A. at the Research Help Desk