The production rates of prompt and non-prompt $J/\psi$ and $\psi(2\mathrm{S})$ mesons are measured using 2.1 $fb^{-1}$ and 11.4 $fb^{-1}$ of data collected with the ATLAS experiment at the LHC, in proton-proton collisions at $\sqrt{s}=7$ and 8 TeV respectively. Production cross-sections for both prompt and non-prompt production sources, ratios of $\psi(2\mathrm{S})$ to $J/\psi$ production, and fractions of non-prompt to inclusive production for $J/\psi$ and $\psi(2\mathrm{S})$ are measured double-differentially as a function of meson $p_{T}$ and rapidity. These measurements are made in a restricted fiducial volume and also corrected for geometrical acceptance after which they are compared to a variety of theoretical predictions.