A bank employee picks up deposits from several individuals and small businesses and brings the deposits to the bank. Some of the individuals own the small businesses and some do not. The deposits include over $10,000 in cash in total. How is the CTR completed regarding conductor of the transactions and beneficiary of the funds?

Without commenting on the wisdom (or lack thereof) or legality of such an arrangement -- the bank employee is an agent of the bank and the deposit is accepted from the individual depositors. You would not aggregate all of the transactions; you would only combine those made on behalf of one person or by one of the individuals from whom the deposits were collected (as if the circuit-riding employee were a teller at one of your brick-and-mortar offices).

Now I'll take the gloves off: Does the bank's insurance underwriter know of this arrangement? Is the employee suffering from some sort of death-wish or need for danger? Has bank management checked out state branching laws to see whether there are provisions for mobile branches that might affect its ability to offer this type of risky service?

To summarize: How you complete the CTR is a very minor issue relative to the other concerns this practice raises.