Assume we have a customer that comes in to Branch A with a $6,000 cash deposit and then later that same day comes to Branch B with a $6,000 cash deposit. We have an automated large currency transaction aggregation report that shows a CTR is required. My question is this:

Should we make an effort to find out from Branch A and B who the individual was that made the two cash deposits, or should we just check "multiple transactions" and leave Section B on the CTR blank?

You should find out who the transactors were.

You should always make your best effort to identify the transactors for a CTR. However, that's not always possible, so you go with the multiple transactions.

I'm assuming that the same person/entity benefitted from both deposits?

You are correct.

I've always made the teller responsible for completing the CTRs check with other branches to find out if they remember who conducted multiple transactions. If they don't remember, we check the "multiple transaction" reason for leaving Section B blank in incomplete. I was getting some flak that this was unnecessary work and that we should just check that box and be done with it. Just wanted to get a sense of whether I'm just being a unreasonable hard nose or not.

Then yes, you can simply check the box off. However, I wouldn't call it unreasonable, as going the extra mile is a good thing.

Since the conductors for our commercial deposits are usually the same people over and over, we have non-accountholder (if applicable) customer records built for them in the system so that we have all required information. If a "new" conductor makes a deposit, the teller is required to build the record at the time of the transaction so that we have all we need to complete the CTR. Then, the teller adds the conductor's name in the transaction description field on the teller system. These descriptions are included in a daily report for the previous day to the BSA Dept. The description is required on all cash deposits to commercial accounts. It took some time, but we now rarely have a teller not include the conductor's name.

If the customer is making multiple cash deposits of under $10,000 the same day, or even over a course of several days, that is structuring, and I would say a SAR would be appropriate.

Hmmmm... That's a stretch. That could be their normal course of business. I have several exempt businesses that meet the $10,000 threshold regularly with multiple deposits a day under $10,000. They make several deposits throughout the day in order to keep their cash levels in the store low. I would do some due diligence before jumping the gun on a SAR.