The Cooler Penning Trap (CPET) at TRIUMF’s Ion Trap for Atomic and Nuclear science (TITAN) facility was developed with a goal to further enhance the precision capabilities of TITAN’s mass measurement Penning trap (MPET) for short-lived radioactive isotopes. The sub-ppb precision of the MPET can be further increased by an order of magnitude or more by using highly charged ions extracted from the TITAN electron beam ion trap as the mass precision scales with the charge state of the species. However, the energy spread induced in these ions by charge breeding may introduce some additional challenges to these mass measurements. By cooling the highly charged ions with room temperature electrons in the CPET, the energy spread can be reduced from a few 10 eV/q to 1 eV/q. We conducted ion injection and extraction simulations with the SIMION package to evaluate the optimum operational conditions of the off-line/development setup and for the integration into the on-line setup. The injection and extraction characteristics of the ion beam were evaluated and the focusing optics were optimized for maximum ion transmission to and from CPET. The effect of different initial ion beam conditions in the trap and various trapping schemes in the optimization of the final beam properties were studied to match the transversal and longitudinal emittance of the cooled ion bunches extracted from CPET to the acceptance of MPET. The simulations showed that the transmission efficiency is sensitive to the axial potential applied to the nested wells, the extraction potential and the length of the ion bunch.