Steve:
Please upload some pictures of the pool and drains, etc. If the returns and skimmers are plugged, there is no water in the lines, then no worries. Your drain, if it has a cover on it, should have been plugged by the builder. It is highly recommended you call the builder first and find out what they did.
It is the responsibility of the builder to winterize the pool properly as the work has not been finished. If nothing has been plugged on the bottom, then ask him/her kindly to come by and remove the covers from the main drains and plug them accordingly. He/She may suggest to leave them open, but this is a discussion that you and the builder must have. Also, you mention 2 drains in the spa? Exactly where are they, and is this a spill over spa?
Again, I would ask the PB to close off all the drains, returns, skimmer lines, etc. Thanks!