We present two complementary strategies for modeling nonlinear quantum optics in realistic resonant integrated optical devices, where scattering loss is present. In the first strategy, we model scattering loss as an effective absorption; in the second, we employ a Hamiltonian treatment, with the loss modelled as a coupling to a 'phantom' channel. As an example, we use these two approaches to model spontaneous four-wave mixing in (i) a ring-channel system and (ii) an add-drop system. We present the rates of photon pairs, broken pairs, and lost pairs for both systems, as well as the full biphoton wavefunction (BWF) including the effects of scattering. We find that for a high-finesse resonator coupled to an arbitrary number of channels, the full BWF can be extracted from the BWF associated with photon pairs in an experimentally accessible output channel.