If free will exists, how will it enter into the simulation (or emulation)?
Short answer: There are many definitions of "free will", and many arguments about the subtelties of the meanings of these definitions. AFAICT, a good argument can be made that making use of some random phenomenon in reaching decisions implements "free will" for the vast majority of these definitions (note that "random" does not need to mean "arbitrarily random"). This answer is not deeply satisfying to me, but a full elaboration of issues would need several pages of text.