This may not be exactly the situation that you describe, but I think the premise is the same. This is directly from the FinCen website:
Question 13b: Would a CTR be required if several individual employees endorsed their respective payroll checks (all individual payroll checks are under $10,000 but combined they aggregate to an amount that exceeds $10,000), and made the checks payable to one employee who, in turn, cashed them at a financial institution for the purpose of distributing the proceeds back to the individual employees?
Answer 13b: A CTR would be required in this instance because one person is receiving more than $10,000 in currency.(10/2001)