It's not easy in the cockpit. We used to use one of those clear course plotters with a compass rose on it. It worked a little better in the cockpit. It's hard on a small boat if you're single handing and have no tillerpilot. Hopefully you'll have a gps of some kind to help out.
We'd keep a chart bungeed down to our small table below and I'd do any real chart work down there out of the wind. I liked using parallel rules best.
I have one of those Maptech fold ups for the Boston area(thanks Marsha!). That's just what I'll buy in the future if I want some paper charts for an area. Very handy.