LewisB this is a similar issue we had because they added the 1100 bags and didn't adjust the timers.

I think your main problem is doing the adjustments while you have water in the bags, tank.

Its best to make the adjustments when the boat says 0%.
you have to remember the timer system is strictly a ON time of the switch, it cant calculate for bad impellers, or air in the system.

I'm not sure if filling while in motion is a good idea for the system. Since its a bottom Feed, if your moving then you would be injecting more turbulence and air in the pickups. The pump will be primed as soon as you drop the boat in the water, unlike the older aerator pumps.

I can agree with you on bottom drain vs the side. What we do is at the end of the day just drain the boat while we put gear away in the water, turn the stereo down real low, you can hear those pumps when they run dry, they make a lot of gargling noises.

I will then run them for a couple seconds on the trailer to make sure its all empty.

Just a couple things i learned so fare.

As for the 100% and 0% if you need to fill at 100% or drain to get the bag to a true 0% you have to keep toggling the switch on and off. We have already had to do this while we get our timers set