Good stuff. They're excellent pumps, and move a lot of air for their size, I think you'll be impressed when you try one out. They also make pretty good pressure, certainly much better than smaller models of diaphragm pumps.
You won't need any check/one way valves with these, they have the valves already built in, but you are quite correct, you can only pump in one direction with these.
The best way to set up the bag system is to inflate the bag before putting the boat in the water, then use the pump to collapse the bag, by sucking the air out, and storing it in either the box, or a separate bottle/tank. Do mind the pressure if you go for the former, as the forces ratchet up very quickly, and boxes are rather 'soft' when it comes to that kind of thing.
To come up just release a servo controlled valve or a solenoid air valve- a fail safe system (well as near as you can get).
The main snag with a compressed air system like this, is that it is impossible to trim for different water densities unless you leave some air in the bag, which of course is squishy, and will compress as you dive deeper. I think this is one of the main reasons modellers moved away from this system.
Some modellers in Germany use compressed air systems for the main ballast tank with smaller piston tanks for trim usually amounting to about 1-2% of the boats overall displacement. These boats offer the advantages of compressed air (e.g. minimal effort to surface and fast evacuation of ballast tank) with the benefits of fine trimming from the piston tanks.