in the latest FinCEN CTR instructions, it give this as an example on pg 96 of how to record a transaction which fits your situation. "For example, if the Part I person conducted a $5,000 deposit into their personal account and a separate $7,000 deposit into the account of another person/entity, there will be one Part I on that person reporting option 2a on the personal deposit with that amount and account number in Item 22 “Cash in amount…â€. There will be a second Part I on that person reporting option 2b on the person/entity account transaction with that amount and account number in Item 22."
In regard to checking multiple transactions, pg 96 says, "Item 3 Multiple transactions: Check Item 3 if multiple cash transactions of any amount totaling more than $10,000 as cash in or more than $10,000 as cash out (cash in and cash out transactions should not be combined) were conducted in a single business day by or for the person recorded in Part I." In your example, two transactions were conducted by the same person and they total more than $10,000 so you would check multiple.