I know that knew in the old EU (see e.g. the ROTS novelization) but is there a source that confirms it in the new canon?
Attack of the Clones actually has him spill the beans to Obi Wan that there is a Sith controlling the Senate. He sure knew!
Yes. See the stare he gives Palpatine in ROTS when he orders Dooku's death. Also, the ROTS novel makes it clear Dooku knows the truth.