The sif's for branch and header should be the same, in accordance with ASME B31.3 App D, which I assume you are using.

Caesar only needs the branch type to be defined once. I have tried on a test model, specifying a reinforced tee + pad thickness only on the header, and only on the branch. In both cases the sif in results were correct for all three legs.

If you enter want to manually enter sif's, you must do so on all three legs of the branch.

Maybe you should try a few tests on a simple model ?