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Hi Tony:
The relative setting of the gain on the plate amp really doesn't tell you much, and I wouldn't be overly concerned about it. The signal strength running from the sub pre-out, the size of the room, the placement of the subwoofer in the room (corner loaded or not), and the location of the subwoofer in relation to the listening position, will all affect the relative amount of gain needed to achieve a given calibration level.
Aside from basic calibration with Avia, it might be good to run a basic frequency response sweep with some test tones, the SPL meter, and the meter correction factors. Or if you want a really rough idea, run the reverse LFE sweep on Avia and look for any major drop-outs in the 30-60 Hz region that might be attributed to room acoustics.
If the FR sweep shows no obvious anomalies, then try upping the sub calibration level a few dB, and keep it in the 25 Hz tune for maximum output in the most common bass regions.
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