Yeah, I believe they're for leveling signal strength of each channel. For example, if the left is just a bit stronger than the right (e.g., b/c of a difference between tubes), you can dial down the left to get the two channels to match.
IIRC, PB suggested to me somewhere on this forum that they can also permit you to boost the SNR of the BeePre (and presumably any other tube preamp): turn down the trim pots on the Kaiju and open up the attentuators on the Beepre. I *think* this increases the strength of the signal coming out the BP relative to the amp's noise floor. But if the noise is already part of the signal before reaching the BP, this won't help.
I keep my Kaiju trimpots fully open (or, more precisely, a degree or two of rotation under fully open - just as a precaution b/c I've noticed that some trim pots can act a little weird at their absolute extremes. But I haven't noticed any weird behavior from the Kaiju PEC pots.
cheers, Dderek