This research delves into investigating ion transport behavior within nanochannels, enhanced through modification with a negatively charged polyelectrolyte layer (PEL), aimed at achieving superior control. The study examines two types of electric fields─direct current and alternating current with square, sinusoidal, triangular, and sawtooth waveforms─to understand their impact on ion transport. Furthermore, the study compares symmetric (cylindrical) and asymmetric (conical) nanochannel geometries to assess the influence of overlapping electrical double layers (EDLs) in generating specific electrokinetic behaviors such as ionic current rectification (ICR) and ion selectivity. The research employs the finite element method to solve the coupled Poisson-Nernst-Planck and Navier-Stokes equations under unsteady-state conditions. By considering factors such as electrolyte concentration, soft layer charge density, and electric field type, the study evaluates ion transport performance in charged nanochannels, investigating effects on concentration polarization, electroosmotic flow (EOF), ion current, rectification, and ion selectivity. Notably, the study accounts for ion partitioning between the PEL and electrolyte to simulate real conditions. Findings reveal that conical nanochannels, due to improved EDL overlap, significantly enhance ion transport and related characteristics compared to cylindrical ones. For instance, under ηε = ηD = 0.8, ημ = 2, C0 = 20 mM, and NPEL/NA = 80 mol m-3 conditions, the average EOF for conical and cylindrical geometries is 0.1 and 0.008 m/s, respectively. Additionally, the study explores ion selectivity and rectification based on the electric field type, unveiling the potential of nanochannels as ion gates or diodes. In cylindrical nanochannels, the ICR remains at unity, with lower ion selectivity across waveforms compared to conical channels. Furthermore, rectification and ion selectivity trends are identified as Rf,square > Rf,DC > Rf,triangular > Rf,sinusoidal > Rf,sawtooth and Ssawtooth > Ssinusoidal > Striangular > SDC > Ssquare for conical nanochannels. Our study of ion transport control in nanochannels, guided by tailored electric fields and unique geometries, offers versatile applications in the field of Analytical Chemistry. This includes enhanced sample separation, controlled drug delivery, optimized pharmaceutical analysis, and the development of advanced biosensing technologies for precise chemical analysis and detection. These applications highlight the diverse analytical contributions of our methodology, providing innovative solutions to challenges in chemical analysis and biosensing.