Half-supply is a good place to start and from there you could tune by ear.
But I find the best and most accurate way is to audio-probe each bbd output. The 'probe points' are clearly labeled on the pcb. There's one for each bbd output:

Apply a sine wave, 400hz for example, to the input of the pedal.
By lack of proper testing equipment I simply record a sine wave from my laptop into a Ditto looper pedal.
Then I use a regular audio probe (piece of shielded wire) for each bbd output test point.
The audio probe, again for lack of better testing equipment, goes to a USB audio interface to a DAW on my computer (= DIY oscilloscope). I use Reaper, running a real time frequency plot plugin. (Span Voxengo).
Now for the interesting part:
-a misbiased bbd gives a distorted output at the probe point
-more distortion = more harmonics
-turn the trimpot until you see the least amount of harmonics in the real time frequency plot: the least amount of spikes at the multiples of your input sine wave...
Repeat for each bbd. Takes 5 minutes.
The clock frequency is cancelled out by combining/mixing the two out of phase bbd signals at the end. There's a probe point for that as well.
When the mix is not exactly 50/50 you'll see a big spike at the clock frequency in the real time frequency plot. Turn the clock trimpot until that peak is at its lowest.
The last trimpot is usually for the repeats/regen. Set it so that oscillation only occurs near the end of the repeats pot.