When I compare execution plans of stored procedures, it only does the first one. I want to compare query 3 which is the main SP but I just am not able to. Is there a way to do this in SQL Server where I can see the stats on the right Properties window.
There is a 'Multi Statement' tab under 'Showplan Compare Options' that allows you to choose which queries you want to compare:
I'm not sure why it's not shown in the picture you've uploaded.