I've made one basic mission using the system(Scenario: Training Day) and I think it's real swell. But does anyone know if there's a way to change the boards dimensions? I need to make a large 12' or 15' long map for a event I want to run.

Also, when marking zones using the shaded box tool, is there a way to change the shaded boxes color?

you can change the shaded color by double clicking.. although that seems a bit buggy. Its in the tutorial I believe.