We have a number of customers that have one bill to address but multiple ship to addresses. What is the best practice for handling customers like these?

Quote from BurrKing_Mfg on 01/17/19 at 13:00:54:

 
We do similar. For customers that just have one Ship-To we just add a "-S" to their code. For others is may be "-S1", "-S2" etc or "-FL" for Florida, "-ME" for Maine, or whatever makes sense.
 
While you can ship to any customer, in the case of the OP where there is one billing address and multiple ships, the Ship-Tos always have "Ship to Customer" set to Y. This prevents someone from entering them as a Bill To. We used to put "Ship Only" customers on Credit Hold but this is cleaner and IIRC you also get a message telling you who the Bill To is.