I am creating a AT5 file. My question is coming into play when I have a large lake (Lake Ontario).... My Mosaic has only 2 small pieces, but they are very far apart.... It seams to take forever to create the AT5 file. Is this normal? Should I create 2 AT5 in this scenario? or can they be on one shaded relief file?

Producing a raster image might take a while on a lake the size of Lake Ontario depending on the detail specified.

It'd be a lot faster to produce these as 2 separate images if there is a significant gap between the two mosaics.

Reefmaster adds in a background image so the background image and both images are processed at whatever resolution is specified.