The manual for you guitar (link above) gives recommendations on adjusting pickup height and sustainer potmeters (in the sustainer cavity at the back of your guitar). I think it would be wise to follow them, and experiment a bit to find the settings which work best for you.
When the sustainer is active, the bridge and middle pickups are not active. The sustainer works only through the neck pickup. In the manual, there is a recommended height for the neck pickup, and you are advised to adjust the middle and bridge pickups to match your neck pickup after it has been adjusted properly.
Like you may have noticed, this guitar, like all electric guitars, resonate and sustain more when played through an amplifier at concert or rehersal volume with proper gain settings. This will also affect a guitar with a sustainer, and provide it with more acoustic resonance to work with.
My advice for you is to read the manual carefully and do some trialing and erroring until you find your favorite settings. As long as .00909 strings are provided with the guitar, I doubt thicker or thinner strings will be a huge improvement. However, like on all guitars, it's important that the strings vibrate freely, that they are clean and that there is nothing - like dirt or lint - dampening them, especially at the points where they're in contact with the bridge and the nut.