John,
I was caught out by the instability when Marlin was in the test tank. I submerged her - all was ok - turned away for a second, looked back and she was on the way to a full capsize! Managed to catch her before any harm was done, luckily!
One big problem you will have trying to pump several ballast tanks individually is finding space for the pumps! Despite such a large model, the space for pumps/motors/batteries and electronics is really restricted. I just managed to fit 2 pumps, bowthruster, aux battery, 2 esc's, 4 switchers and 8 ch rx in the forward space, and in the rear was the main battery, 2 pumps and main drive motor.
The 4 tank system I used gave me control of the boat in all directions when submerging and floating up. I found that submerging and floating up stern down a little gave the best control. I fitted my pump suctions at the stern of the tanks for this reason so I could get most of the water out. (there was always a little left in to pump out when on the stand.)
Interestingly, the full size Blue Marlin submerges stern first as well, for the same reasons.
I looked for small (6mm/1/4") solenoid operated valves to enable me to direct pumped ballast as required, but, I couldn't find anything that didn't cost the earth.
Ian