In the new PC app, I would suggest you use the Approach Grid to judge your distances. I would not use the width of the aiming box like you do on Flash.
You can set the Approach Grid to ON in your Settings. It's the 3rd option under Game.
When you have the Approach Grid set to ON, you will see a grid when you click or move the aimer on approach shots. The grid will either be 9x9 or 15x15. If it is 9x9 (larger squares), then each square is 3 yds. If it is 15x15 (smaller squares), then each square is 2 ft.
The calculations you do to adjust for the wind speed and direction (if that's what you mean by "clock") should be the same for the PC app as they are for Flash.
Hope this helps.