I can add a comment about spray skirts on northern trips. Their usually isn't any room left for flotation bags on these trips, and the best skirts are heavily built.

Preacher makes some good points. Bags or skirts both work, I've gone both ways. If you go with bags, just finish filling your boat with air bags, for and aft of your gear. Might not be necessary for "pool & riffle" stuff, but if you progress into bigger stuff, definitely do it. Another plus for spray skirts is they're warmer. Besides keeping you drier as you travel, they're handy for stuffing things under them that you want to keep dry and the skirt can be pulled up as a quick windbreaker.