We have a CTR on a business customer who had multiple night deposits over the weekend totaling in excess of $10,000. So would we check 3 in section 1 and also check aggregate in #24 since all of the transactions were under $10,000 but aggregated over $10,000.

Review the instructions for the "aggregate" box...you do not check it unless at least one of the transactions was conducted through a teller. Your excuse for not identifying the person conducting the transactions was provided by checking "night deposit."