I think your best bet if you want to use 2 pumps for the whole system is to dedicate 1 for filling both bags and then 1 for emptying both bags. A Tsunami 1200 might be able to fill 2 at once if you run a Y and use the same length of tubing from the y to both bags. Water is funny and will follow the path of least resistance(just a guess, no real world experience and someone may know different). Another option would be to run a T and then use shutoff valves on both sides and then shut off one side and fill and then open and shutoff the other side and fill. As far as draining, I think you could get away without the shutoff valves, maybe built a manifold that both sacs dump into and then the pump sits on the manifold and it doesn't care where it gets it's water from, it will just pump it out. For the drain, you might want a check valve on both sides of the manifold to keep water from the other sac from pushing back up to the opposite one if that matters at all to you.
I found Tsunami 800's for $26 for my system: http://www.backtoboating.com/Scripts...p?idproduct=80
They also make a dual output Tsunami: http://www.backtoboating.com/Scripts...p?idproduct=81
It sounds like you are on a budget, you could always run 1 800gph for each fill (2 total) and then get 1 1200 to handle your drain and it might be a little easier on you.