Hi Nathan,
I can't speak to your specific perspective problems without seeing your scene. Might this just be because the calibration cubes are oriented in a way that you don't find "useful"?
I should also warn you to be careful about scrolling in too far, because it's possible to pass "through" your markers and view them from the other side (thus flipping right-handed to right-handed coordinate systems). Always check that the axes (and morphology) in the 3D viewer make sense and aren't mirrored.
When in doubt, I suggest exporting your point coordinates and importing them into Maya. It's easy with the imp shelf tool set to the xyz Translation data type. We've always gone that route, often repeatedly, when trying to sort out point identities in complex scenes with over 100 fast moving markers.
Good luck,
Steve