It really depends on your room, but our recommended setting would be to set the sub volume around 9 o'clock. Though, admittedly the sub is less sensitive as it was before, it is still fairly sensitive, so setting the sub upwards to 12-1 o'clock is generally a fairly high setting. However, it is worth noting that it also depends on the level that the sub is receiving from the receiver as well. For example, in many cases, the LFE channel level can go from -12 to +12 dB (24 dB difference). Sometimes it can be more than that, but that setting determines how much voltage is being sent to the sub. All things being equal, +12 on the LFE setting would mean that you wouldn't be able to turn up the volume on the sub as much before it starts to hit its limits versus having a -12 dB setting. Sensitivity of the speakers and the type of material being played also have an impact on that as well.
You are correct in that a higher setting of volume on the sub means that you don't have to turn up the channel level as much from the receiver end to get the same output. However, if you run the auto-calibration software and the LFE level is set to 0 or below, then it won't matter as much. So what I would do, if the receiver doesn't have you set a level on the sub to begin with, is run the calibration with the volume a 9 o'clock. After that, check your speaker settings to make sure your speakers are set to small, 80 Hz crossover is generally a good starting point unless your speakers are on the smaller side (4" midrange and below). Also check your channel levels. If the receiver set your sub to -12 and your speakers are around 0, that means your sub is set to high, if it is set to +12 and your speakers are set to 0, your sub is set too low.