On the Closing Disclosure, if we contract for a service, and that service is then sub-contracted out by the initial contractor, who do we as a bank list as "to whom payable"? (In most cases, our funds are being paid to the contractor and they are paying the sub.)

It would be who you cut the check too.

I would think your check should be cut to your vendor and not the subcontractor that you have no direct relationship with. However, check the terms of your contract with your vendor. Maybe it stipulates that you would pay their subcontractors directly.