It is the receiver mfg that sets a speaker to small or large, not the setup feature. Correction tools like Audyssey and others measure the speaker (in Audyssey's case the -3dB point) and report it back to the manufacturer. For Audyssey if a speaker measures a 40hz or better -3dB point then it usually is set to Large.

Anyway, to answer your question, you still want to change those to "small" since you have a subwoofer in the mix.

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