We present an approximate deconvolution (AD) large eddy simulation (LES) model for the two-layer quasigeostrophic equations. We applied the AD-LES model to mid-latitude two-layer square oceanic basins, which are standard prototypes of more realistic stratified ocean dynamics models. Two spatial filters were investigated in the AD-LES model: a tridiagonal filter and an elliptic differential filter. A sensitivity analysis of the AD-LES results with respect to changes in modeling parameters was performed. The results demonstrate that the AD-LES model used in conjunction with the tridiagonal or differential filters provides additional dissipation to the system, allowing the use of a smaller eddy viscosity coefficient. Changing the spatial filter makes a significant difference in characterizing the effective dissipation in the model. It was found that the tridiagonal filter introduces the least amount of numerical dissipation into the AD-LES model. The differential filter, however, added a significant amount of numerical dissipation to the AD-LES model for large values of the filter width. All AD-LES models reproduced the DNS results at a fraction of the cost within a reasonable level of accuracy.