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If I understand you correctly, the air will tend to take the path of least resistance. You are correct in thinking that the box plenum underneath would be better. As far as operation, what are your pressures, temps ? You are in fact cutting off half of the coils capacity and as a result this should be evident on your test results. I am curious to know what the R/A and S/A readings and also the wet bulb on the discharge of the coil.