Hello Jennifer,
please look for ‘Reconstruction Region’ section in the application help (you can access the help via F1 shortcut).
There should be detailed guide how to use this tool.
To create box, just use left mouse button, move cursor, click, move click 
If you can’t do it this way, there is probably some other problem.
To overcome this issue, you can also create reconstruction region automatically and then edit it using box widgets.