In this paper, we presented path tracking error comparison between two navigation schemes for underwater glider that combine path planning and a path tracking controller. Path planning is performed with the time-averaged flow field for both schemes, while path tracking is performed with the instantaneous or the time-averaged flow field. Mathematical analysis and numerical simulation show that performing path tracking control with instantaneous flow results in smaller path tracking error when the strength of spatially varying flow is small compared to glider speed, while it leads to larger path tracking error if spatially varying flow is the same order as the glider speed. Performing path tracking control with instantaneous flow leads to less path tracking error when the spatially varying flow is of relatively high frequency, but it produces larger path tracking error if the spatially varying flow is of low frequency. Simulated experiments near Cape Hatteras, NC show that in this specific region, performing path tracking control with instantaneous flow results in less path tracking error, which is consistent with the analytical result.