FinCEN had a Scenario like this on a webinar. This was the response:
Q: In the FinCEN CTR, when would I use the “Multiple Transactions” box and the “Aggregated Transactions” box?
Scenario II:
A bank receives two night deposits (each transaction below the reporting threshold) that totaled over $10,000 that are to be deposited into one business account.
The financial institution would file a CTR by completing a Part I on the entity to which the account, where the funds being deposited, belongs by selecting Item 2c (Person on whose behalf transaction was conducted) and Item 3 (Multiple Transactions). Additionally, the financial institution would select “Night Deposit” in Item 24 as no identifying information on the transactor was collected; “Aggregated Transactions” would not be selected in this scenario as none of the deposits was a teller transaction.
The slides for the webinar can be found at
http://www.fincen.gov/whatsnew/pdf/CTR&DOEPRecordedVersion-PDFslides.pdf