Not if you soak them separately. If you want to toss the whole thing in the water, they should be attached to a tank and pressurized. The seat saver in the 2nd stage only seals when the system is pressurized. That means that the rest of the time, that seal isn't under compression so it lasts longer. Part of why the service intervals on atomics are longer than average. The trade off is that when the system isn't pressurized, water could get in to the 2nd stage, migrate up the hose, and get in to the 1st stage where corrosion could start. By soaking the first stage first and then the 2nd (preferably with the first stage elevated so water can't go up the hose), you limit the chances of water getting into the first stage.Do they have to stay pressurized the whole time (attached to a tank)?
It sounds more complicated than it is. It's nothing more than a different cleaning routine.