Geographic regions as subpopulations/demes
It is impossible to answer your question in the general sense. Yes, detailed population structure may matter. It very much depends upon what your question is and what parameter space you are willing to answer but it is possible that assuming panmixis would be unrealistic.

Note that accurate data on $F_{ST}$ won't suffice to estimate migration rate $m$.

Note also that many simulation platform already exist and you might not have to reinvent the wheel (see Sequence evolution simulation tool).