Altium has a feature called Polygon Manager. While I know CS isn't meant to be Altium, I feel that the ability to control the pour order of your polygons is a very important feature that should have some sort of GUI, rather than manually pouring one at a time to make sure a high level pour will not pour over a lower level pour on the same layer. Some boards have many different polygons and then one overarching ground pour, etc. and the current process for making sure all the pours are on the board is tedious and error prone.
Please consider adding a Polygon Manager GUI of some sort.
Thanks!