We test state-of-the-art model atmospheres for young low-mass stars and brown dwarfs in the infrared, by comparing the predicted synthetic photometry over 1.2-24um to the observed photometry of M-type spectral templates in star-forming regions. In both early and late young M types, the model atmospheres imply effective temperatures (Teff) several hundred Kelvin lower than predicted by the standard Pre-Main Sequence spectral type-Teff conversion scale (where the latter is based on theoretical evolutionary models). We postulate that in the early M types this discrepancy arises from remaining uncertainties in the treatment of atmospheric convection, whereas in the late M types it is likely due to an underestimation of dust opacity in the atmospheric models and an attendant overestimation of H2O opacity, due to insufficient backwarming by dust. Using the synthetic spectra to estimate stellar properties leads to reasonably accurate bolometric luminosities (Lbol), but overestimates radii (due to underestimated Teff) for the early and late young M types compared to evolutionary theory; this then leads to underestimations of age and mass, which we demonstrate for a large sample of young Cha I and Taurus sources. By selecting the model atmospheres which best represent the true stellar continuum at each spectral type, we then go on to infer the disk parameters for a selection of young, low-mass disk-bearing objects in Cha I by modelling the IR SEDs (again over 1.2-24um) using the radiative transfer code ttsre, coupled to the machine learning code skynet and a Bayesian parameter estimation. Just over half of the sample are able to be accurately fit by the analysis. No noticeable level of correlation is found between the extent of settling and grain growth in the disk and the stellar mass, an interesting result given the lessened gravitational/luminosity effects that lower mass objects should have on their disks. No correlation was also found between the disk thickness and accretion rate (a tracer of the system age), which, when coupled to the fact that a wide range of disk flaring indices are found, suggests that grain growth/settling occurs over a rapid timescale in the disk's early evolutionary sequence.