I have a company here installing a Payne Heating unit in a 3 ton system. Does it matter which side of the unit that the return air hole is cut in? I heard it should flow out the bottom or right side. Can you tell what is most efficient?

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First off, follow install instructions. But as far as I know, it doesn't matter where the return opening is, as long as it is big enough, and, of course, cut into the blower compartment. Left, right, back or bottom, as long as there is sufficient airflow.

Who is telling you it needs to be on one side or the other for efficiency? Ive never heard of that in the many years Ive been in the trade.

I really think, since you hired a pro to install the furnace, you should let them do their job, and of course do ask them if you have any concerns and see what they have to say.

If it's a up flow unit either side will work. If its down flow or horizontal installation the rules change.