The answer here is "maybe".

Simply burying a model will not cause CAESAR II to alter the B31.3 stress computations. However, you could also:

a) Throw the "Include F/A" switch in the Configuration, or
b) Throw the "Use Appendix P" switch in the Configuration.

I'd suggest playing with a very small model to get an understanding of what is going on before jumping in to your real model with both feet .