  A key question in extragalactic studies is the determination of the relative
roles of stars and AGN in powering dusty galaxies at $z\sim$1-3 where the bulk
of star-formation and AGN activity took place. In Paper I, we present a sample
of $336$ 24$\mu$m-selected (Ultra)Luminous Infrared Galaxies, (U)LIRGs, at $z
\sim 0.3$-$2.8$, where we focus on determining the AGN contribution to the IR
luminosity. Here, we use hydrodynamic simulations with dust radiative transfer
of isolated and merging galaxies, to investigate how well the simulations
reproduce our empirical IR AGN fraction estimates and determine how IR AGN
fractions relate to the UV-mm AGN fraction. We find that: 1) IR AGN fraction
estimates based on simulations are in qualitative agreement with the empirical
values when host reprocessing of the AGN light is considered; 2) for
star-forming galaxy-AGN composites our empirical methods may be underestimating
the role of AGN, as our simulations imply $>$50% AGN fractions, $\sim$3$\times$
higher than previous estimates; 3) 6% of our empirically classified "SFG" have
AGN fractions $\gtrsim$50%. While this is a small percentage of SFGs, if
confirmed, would imply the true number density of AGN may be underestimated; 4)
this comparison depends on the adopted AGN template -- those that neglect the
contribution of warm dust lower the empirical fractions by up to 2$\times$; and
5) the IR AGN fraction is only a good proxy for the intrinsic UV-mm AGN
fraction when the extinction is high ($A_V\gtrsim 1$ or up to and including
coalescence in a merger).
