I read it a little differently.
He didn't order 6 men to put on ordinary jackets, he order 6 men that were already dress as sailors, already in ordinary jackets to get into the boat.
The only people actually quoted as changing into other clothes, or into a disguise are "he himself", the master, and the doctor. Interesting that their disguise is to "dress up" like gentlemen.... leading us to believe that even in these positions of authority, they were not already dressing like gentlemen.
So another way to write it would be "we told six regular sailors in their ordinary sailors clothes to get into the boat, while we dressed up like gentlemen so we would appear to be more like a regular merchant ship and crew.
Certainly makes sense from the sentence structure...