That won't change a thing. Audyssey auto setup ignores all settings, the point of calibrating is to check what your system is capable of. If you set your speakers to small or large before Audyssey, it will just ignore that and go through the auto setup.
Further, each speaker is calibrated *independently* from the others. Each speaker is set to a level that has it outputting the correct volume (75dB with the standard test tones) and gets its own EQ filter, so the other speakers you have will not impact what happens to the sub.
Since you got a -3.0dB for the sub then your system is fine and running within spec, you should just start enjoying it. Ensure all speakers are set to small (again you do this AFTER calibration not before) so bass gets routed to the sub.