Replacing 12 x (internal) CR2032 batteries with one (or more) external batteries
I'm afraid that a standard 9V battery may not power your lights any longer than the 12 coin cells. I am also concerned that if you connect several lights in series they may not flicker properly.

Is there a possibility that you could use an AC-to-DC converter (a "wall wart") to provide power? I know that would mean a wire running into the aquarium but it would save a lot of batteries. If not then you might consider using 2 or 3 D-cells in series. You should be able to get a plastic holder for these batteries at a local hobby shop.

Either way, you need to have a source of low voltage (3V to 6V, say) at fairly high current. Then I think you need to connect a resistor in series with each light, and connect all of the light/resistor combinations in parallel. The resistor is needed to limit the current to each light, something that the coin cells did inherently because of their low current capability. I would suggest that you start with about 100 ohms if the supply is 3V and 500 ohms if it is 6V.
If the light is too dim or doesn't flicker then gradually reduce the resistance until it behaves properly. It might be a good idea to try this with just one light until you figured out a good resistor value, but you will need one resistor per light in the end.