Since we don't have a "Transparency" option, it will be OK if you overlap two contours which have contour line only, without filling any color. For example, suppose you have two matrix, Matrix1 and Matrix2:
1. Active Matrix1 and select "Plot --> Contour Plot --> Contour B/W Lines + Labels" to create a contour plot. 2. Right-Click the "1" symbol on the contour plot and select "Layer Contents". And select Matrix2 to "Layer Contents" box. Click OK. 3. Now you can see a overlap contour plot. Specify different color for contour lines to distinguish them.
Note: Before plotting, it will be better to set Matrix1 and Matrix2 in the same XY range.