Where the sides of the tank attach to the bottom of the tank is where the highest water pressure will be. The water will be pushing down on the bottom of the tank which will be counteracted by the support from the stand. The water pressure will also be pushing the sides of the tank out.
With the sides on top of the bottom and screwed up through the bottom the screws will have a shear force that will be supported by the the plywood sides.
With the sides on the side of the bottom the force will be lined up with the length of the screws... which is not nearly as strong, especially in plywood.
I am not saying your plan won't work or even that it is a bad idea... just make sure to secure the sides to the bottom well. A 2" x 2" stick of wood around the inside bottom of the tank that you can screw into from both the sides and the bottom is one way you could reinforce this joint. The strength of the tank will depend on the design of the tank as a whole.
How tall will the tank sides be?