I have heard several different theories. I hear some people say to set it to 1/3 octave below tuning.
There is a more technical process, heres a quote that sums up a good way to set the ss filter.
"The port works as a bandpass filter, so the first thing you must to do is verify the frequency response of your sistem, you can use a decibelimeter or a rta beginning with the lower tone you can use, you must to draw a chart. with the values of your response, with this you will find the peak frequency of your enclosure, once done this you can determinate the frequency -3 dB of the port,
From this value to the lower frequencies, your enclosure works as a infinite baffle, thus there is no damping to the cone, the excursion increases, and the control is minimum. decreasing the amount of sound.
for example: if you detect that the -3dB point is set at the 26 Hz in your chart, you have to use this frequency with a tone generator, and do the next, identify in your chart the peak value for your port and take that value. we can say 90 dB.
use your 26 Hz tone and calibrate your system to get the same 90 dB measured with your dBmeter or RTA, now begin to adjust your subsonic filter up to the position where the amplitude gets 3 dB below your initial value, that is 87 dB. with this action you have adjusted your subsonic filter to the exact frequency where the information begins to waste power with no benefits."
Credit goes to RENAULT10 on diyma. I did fix some of the spelling errors, but even with them he seems to know his stuff.