It's best to think of them as completely separate programs. The earning tables are different, the value of the points is different, the status thresholds are different, and the redemption tables are different.

That they're in the same alliance means in both cases you can earn on any *A flight and redeem for any *A flight. It also means if you reach status on one then you get certain benefits on any *A carrier. But only certain benefits are alliance-wide (lounge access, priority boarding and checkin, not much else -- notably not upgrades).

So you have to pick one to concentrate all the points on one or the other. But you need to evaluate which program will earn you the most free flights and reach status with your flying to decide which one. And you have to check whether there are benefits you want from one that aren't available on the other.