Customer visits the loan department (which is in a separate office building with other administrative offices, is not a branch and does not keep cash). Customer makes a $20,000 cash payment on a loan (ignore thinking about a SAR just this once).

We accomodate the customer by counting and verifying cash. Customer leaves. Two of the loan department employees then right away go to the closest branch to make the loan cash payment and get the cash out of the regular office building. Should the loan department employees, who took the cash to the branch, have their ID entered on a CTR as the conductor, or would it be okay to put the customer's info? Or would it make no difference?

I would list the customer as the conductor, since he is the one who transferred the currency into the bank's posession. Similarly, if a customer comes into a branch, and hands a large deposit to the new account rep at the desk, and the new account rep walks the cash over to the teller line, the customer is still the conductor.

Agreed. The customer goes in Section A (on whose behalf ...) and the "conducted on own behalf" box in Section B should be checked.