heya drax,

imo the two large (12 inch?) air stones are plenty sufficient for the job, and you probably won't notice any difference running the additional water pump. in my setup i use aerospring, which is supposed to have the best oxygen distribution, but in all honesty i haven't noticed much difference when compared to a dwc, which i also have running.

now, sorry to not have answered your question yet. if you've got the extra pump laying around and you're compulsively addicted to perfection (like myself), then feel free to install the pump. from what i gather your water pump will be streaming water up and will be submerged just below the surface. a 90 gph pump is about as weak as they get, so this will not cause you any problems with the roots.