We are having one contractor build/replace our fence and add a new deck. Does it matter if I have our electrical contractor add the plugs/outlets to the decking area after the deck is finished? Or will it be more cost-effective to have the eletrician install the plugs at the same time as the decking is installed?

In general I don't think that it would make much difference.

But sometimes it might be better doing it one way or another depending on type of construction, foundation, access, etc.