You have it right. For a heavily loaded item like a pulpit, an epoxy wedge
followed by a softer sealant is right. If the deck is cored, you should look
at ways of firming up and sealing the bolt holes.

Dan wrote:

What is the proper way to bed deck hardware using sealant?
Do you want to have a thickness of sealant? How thick?
Will the sealant fill gaps?
The pulpit flanges are at a slight angle to the deck. With the flange
sitting on the deck, there is a gap of 3/32" at one end. Will the
sealant fill this gap and provide support, or should I build an epoxy
wedge for support, and set the flange with a thin layer of sealant?

Thanks everyone,
Dan