We have a closing attorney’s office that sent the client here to make the cash deposit of greater than $10,000 for the closing. I am trying to figure out who actually benefited from the transaction. The money was deposited to the attorney’s account, but I tend to think the money really benefits the individual. I remember there being something published about this, but I cannot put my hands on it. Any help would be greatly appreciated.

Administrative Ruling 89-5. You want example #3.

The status of administrative rulings is cloudy, but it's all you will find on the subject so I suggest you follow it.

When I listed the closing attorney and the client name in Sections A, our processing system prepares the names in alphabetical order and lists the closing attorney first. If I want to mark the client as the conductor does this matter since his name is not in the first box? Do I need to put his name in Section B to be certain there is no confusion on who conducted the transaction?

No. Just check the box on page one "conducted on own behalf".