I'm not so sure superglue is aquarium safe, though I might be wrong. Personally, if the bottle/tube/container does not specifically say "aquarium safe" or "food surface safe" it is not going into my fish tank. It simply is not worth risking my fish. Many glues have chemicals that are toxic to fish (and people).
That being said, it sounds like you are trying to sink the wood in a tank that has already been filled with water. If that is the case, most all glues/silicone sealents need to be applied to thoroughly dried surfaces. There are some aquarium safe epoxies that can be applied in the water, though I can not recall any names. Driftwood can take weeks before it is logged enough to sink, and I have read some posts about having to wait months before their driftwood would stay sunken. Patients is key in this hobby. If you can't wait, try some silicone sealant (aquarium safe!!) or if adding to an already filled tank, find some epoxy that can set in water. If you use silicone sealant, you will need to wait at least 24, preferabbly 36-48 hours to let it cure before adding it to water.
\Dan