  Molecular line ratios, such as HCN(1-0)/HCO$^+$(1-0) and HCN(4-3)/CS(7-6),
are routinely used to identify active galactic nuclei (AGN) activity in
galaxies. Such ratios are, however, hard to interpret as they are highly
dependent on the physics and energetics of the gas, and hence can seldom be
used as a unique, unambiguous diagnostic. We used the composite galaxy NGC 1068
as a `laboratory' to investigate whether molecular line ratios between HCN,
HCO$^+$, and CS are useful tracers of AGN-dominated gas and determine the
origin of the differences in such ratios across different types of gas. Such a
determination will enable a more rigorous use of such ratios. First, we
empirically examined the aforementioned ratios at different angular resolutions
to quantify correlations. We then used local thermodynamic equilibrium (LTE)
and non-LTE analyses coupled with Markov chain Monte Carlo (MCMC) sampling in
order to determine the origin of the underlying differences in ratios. We
propose that at high spatial resolution (< 50 pc) the HCN(4-3)/CS(2-1) is a
reliable tracer of AGN activity. We also find that the variations in ratios are
not a consequence of different densities or temperature but of different
fractional abundances, yielding to the important result that it is essential to
consider the chemical processes at play when drawing conclusions from radiative
transfer calculations. From analyses at varying spatial scales, we find that
previously proposed molecular line ratios, as well as a new one, have varying
levels of consistency. We also determine from an investigation of radiative
transfer modelling of our data that it is essential to consider the chemistry
of the species when reaching conclusions from radiative transfer calculations.
