Technically speaking, you can't. Because class organisation rules are associated with the application in one to one relationship.
Though, I could sense your requirement to be implemented in a little different way.
You could have two different access group mapped to same application, I know it won't serve your purpose fully but at least it may give two sets of user with different master settings( I am pre-assuming it as look and field and functionality).
Hope it helps you, kindly notify us by marking this post as answered for the larger Pega audience.