:...I wonder whether it's best to do the deck
: and hull separately, or if I should hang the kayak to be able to
: do both deck and hull at the same time?

Mark, I brush varnish (or now use 2-part Polyurethane) both the deck and hull at the same time, except for the final coat. I hang the boat, and work around the boat from bow to stern. It helps to wet the floor so humidity is high to keep a good wet edge.

For the final coat, I mask off at the shear line and do the hull only. I immediately take the tape off. The next day, I mask it off again and do only the deck. I also like to have an assistant follow me around on the final coat to check quality.

Good lighting is essential for a good varnish job.

John
http://www.outdoorplace.org/paddling/