I had a PP/zbox in a carbed boat. You will never get the response of throttle by wire injected boat but PP gives you all the information to get as close as possible with the technology you have. Make sure you have good throttle return spring. There is a big thread here about the ball timing @Windsurfnut is talking about.
As far as mapping goes, if the course shifts significantly when current changes you could just map it as a second course. This would assume that the current is consistent when it is present. But really, I doubt that the balls move very far unless it’s a pretty strong current.