i'm still debating with myself how many more advanced editing features to add to SC.
The program is designed to work well with an external graphics editor -- the best solution might simply be to get yourself a good image editor like Paint Shop Pro, and configure it in SC as the image editor (see options). Then whenever you need to do something like set transparent area, you can just hit the graphics editor button on the top right of SC, then edit and save the modified image, and SC will pick up the changes. SC will even preserve any objects (arrows, callouts) that you created on your original.