Motivated by recent experimental results that reveal rich collective dynamics of thousands-to-millions of active liquid crystal skyrmions, we have developed a coarse-grained, particle-based model of the dynamics of skyrmions in a dilute regime. The basic physical mechanism of skyrmion motion is related to squirming undulations of domains with high director twist within the skyrmion cores when the electric field is turned on and off. The motion is not related to mass flow and is caused only by the reorientation dynamics of the director field. Based on the results of the "fine-grained" Frank-Oseen continuum model, we have mapped these squirming director distortions onto an effective force that acts asymmetrically upon switching the electrical field on or off. The resulting model correctly reproduces the skyrmion dynamics, including velocity reversal as a function of the frequency of a pulse width modulated driving voltage. We have also obtained approximate analytical expressions for the phenomenological model parameters encoding their dependence upon the cholesteric pitch and the strength of the electric field. This has been achieved by fitting coarse-grained skyrmion trajectories to those determined in the framework of the Frank-Oseen model.