Organic Mixed Ionic-Electronic Conductors (OMIECs) are materials that are composed of 𝜋-conjugated polymers and an electrolyte solution. They have interconnected electronic and ionic transport due to reversible doping by ions within the electrolyte solution and delocalized electrons within the 𝜋-conjugated polymers. Their unique structure allows them to be used in electronic devices. The conductivity of OMIECs can be improved by changing polymer morphology, which can be accomplished through doping. The morphology of 𝜋-conjugated polymers is also affected by ion-electron coupling in OMIECs. So, an optimal design that considers both ionic and electronic pathways is necessary to improve the conductivity of OMIECs. From a design perspective, changing the components of the electrolyte and potentially improving the OMIECs is highly attractive due to the relative simplicity of swapping out these components. However, even small changes in the electrolyte, such as varying the size of the anion, can have a cascade of effects on OMIEC morphology, doping efficiency, and charge transport which are still poorly understood. This work adapts and extends OMIEC coarse-grained molecular dynamics (CG-MD) simulation methods recently developed by the Savoie group to elucidate electrolyte-function relationships, and kinetic Monte Carlo (kMC) simulations to examine the anion size and side-chain design effect on the conductivity of OMIECs through calculating polaron mobility. The results demonstrate the impact of anion size on polaron mobility and polymer morphology across three different scenarios: polymers with highly polar side chains at full frequency, intermediate polar side chains at full frequency, and intermediate polar side chains at half frequency. We observe that charge transport is primarily governed by a lower side-chain frequency, which significantly reduces trap site formation. In contrast, the effects of anion size and side-chain hydrophilicity are comparatively minor. These findings provide valuable insights for developing general design rules for the OMIECs with wider class of polymers and dopants.