umm, how about try taking a picture of a bright star, then make a small move on the mount in one axis to move the star a few pixels and take another? If you then repeat with the other axis, you would have several images that you could overlay as layers in Photoshop/GIMP and get the line designating the trajectory of the star in each axis? I don't know how scientific that would be, but it should give you two lines (L-shape) that are quite close to perpendicular - I cannot imagine they won't be unless your mount is damaged somehow….
As for the telescope, are you asking about the polar scope built into it? If so, what model and brand mount is it?