How do I add additional layers of attic insulation to a joist cavity
that is only half full?

If joist cavity is only half full and the recommended insulation level
in your area is R-38, fill the joist cavity flush with the top with the
appropriate thickness of fiber glass insulation. Then lay a second
layer of unfaced insulation perpendicular to the existing layer to give
a total of 12" (or an R-value of 38) in the joist cavity. Covering the
attic joists with the second layer will reduce heat loss through the
wood.
as it says at:
http://www.owenscorning.com/around/i.../faq_attic.asp