Sub application/key board short cuts

Ok, 2 questions here.
1. I am making a program to help organize stuff, so I wanted it to open your programs for you, but It only works if the window is selected. Any way around this?
2. This is for the same program. When I try to open a sub-application, it works sometimes, but not all the time. It also puts all these empty folders where my application is being made. What object should I use? I have used the regular event, plus using the Vitulize object, and the File-Folder object.