I would expect that if air is moved across a larger area of your tank, then it would help a bit more in terms of cooling your tank. So in this case, then yes, I think mounting the fan on one end of your canopy blowing across the surface of your tank would be more effective. Just keep in mind that using a fan as a means of cooling your tank will lead to an increase in evaporation. I'm not sure if two fans are needed for your tank, experiment with one first.
-Richer
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