I am trying to understand GPO

I understand what a GPO is used for and I can’t seem to get it to work.
First I had setup a OU called everyone. In it I created a GPO that had a startup script that mapped everyones drives for them. It never worked so I had to put it at the site level. And that works fine now.
Now I have a special groups for a software program that needs to be installed on selected computers. Yes I have added them to the OU. I had added the msi file to the computer section under software installation package. I can’t get this GPO to run in just this group. Unless I move it to the top of the site. But then I will install on everyones computer. Please help!!!!