After you have successfully set up the position you desire, you can now analyze the position. You can click Hint in the toolbar to get the best move of cube decision in the same way as described in the chapter called Playing a game. Hint, rollouts and evaluations done from the hint window will not be saved if you try to save the position. If you want to analyze the position and then be able to save the position and the analysis results you should rather do a move and then click back to the move and then choose Analyze->Analyze move for the menu. You can then work in the analysis pane on the right side instead of in the hint window.
You can enter checkers on a point by clicking on the point. Notice the amount of checkers you add on a point, depends on where on that point you click. Left mouse button, black checkers and right mouse button, red checkers. (assuming you didn't change the colors). You will get used to this editing. and it makes it much faster to set up a position.
See also Albert Silver's post on GammOnLine