I set mine so that the outputs for each pickup were balanced, as I most often play with both of them engaged, but also turned down enough so that the overall output was not vastly louder than my other two Alembic basses that are not Series-equipped. (if that makes any sense...) I often switch between them, and this keeps me from having to adjust input gain at the amp or preamp point. These Series basses send out a really 'hot' signal.
In short, I don't think it matters what level the gain for each pickup is set to, only that you dial out the inherent hum at that setting with the inner trimpot to that pickup. Maybe start with the gain trimpots in the middle of their sweep, and adjust from there? Just remember to do one at a time.