Only if you ran the auto-EQ setup or manual EQ setup with the SMS-1 set to a specific preset (rather than "setup") would the EQ settings be saved to only that specific preset. By default, however, both auto-EQ and the manual adjustments are done under the "setup" preset, which means that the exact same adjustments are applied to all five presets. At that point, the only differences between the presets are those described on the System Settings screen (including one additional EQ and different volume levels).

Bottom line: preset 4 is the default preset for the SMS-1. By default, presets 2, 4, and 5 all purely output your custom EQ curve with no additional changes. You can use any of the five presets and get your custom EQ curve (preset 6 being a bypass of the entire EQ section), but presets 1 and 3 will by default apply an extra boost to the curve (5dB at 35Hz for preset 1 and 3dB at 55Hz for preset 3) as well as a volume boost to the entire sub signal (5dB for preset 1 and 3dB for preset 3).