Our research investigates the impact of auxiliary structures on ion transport in electrochemical systems such as batteries and microscale desalination units, whose importance for sustainable development has increased dramatically in recent decades. The electrochemical systems typically feature ion-selective surfaces, such as electrodes and ion exchange membranes, where ion depletion can cause performance issues including metal dendrite formation and flow instability. Recent research has shown that auxiliary structures in these electrochemical systems can enhance ion transfer near ion-selective surfaces, thereby resolving the instability problem and improving the energy conversion efficiency of the system. Our study leverages recent advancements in nanoscale electrokinetics to model these auxiliary structures as pillar arrays near an ion exchange membrane in a microchannel. We examine how these structures enhance ion transports relative to the characteristic length scale of microchannel depth and pillars' proximity to the ion-selective surface. Results show that the effect of the pillars varies significantly with their placement. Specifically, in deeper microchannels, where electrokinetic convection is stronger, the closer the auxiliary structure is to the ion-selective membrane, the better the ion transfer. However, in the thinner microchannel, the proximity of the auxiliary structure to the ion selective membrane has a less significant correlation with the ion transfer. Therefore, this finding highlights the importance of spatial arrangement of the auxiliary structures in improving the performance of electrochemical devices. Conclusively, this study can help to better understand energy conversion systems such as fuel cells, salinity gradient power generation systems, and electrochemical desalination systems, where auxiliary structures can be used in the vicinity of ion-selective surfaces. Especially, our fundamental electrokinetic study provides an effective means for designing the efficient electrochemical platforms utilizing micro/nanofluidics.