We have a loan in the works where the property has two buildings on it that are in a flood zone. We know that our flood insurance required is going to be the loan amount as its the lesser of the three "options". How do we properly allocate enough flood coverage to each building when the flood coverge that we will require is less than the replacement costs of both buildings together?

Leave it to the borrower. It is their insurance - all you care about is that you have the proper total amount of coverage.