I will be making 200 gerber daisies for a cupcake wedding next Fri. The flowers will be various shades of pink with brown middles. I am planning on starting them this week.

What is the best way to store them until I put them on the cupcakes?

Not sure how big yours will be but have you thought of an egg carton?

I think they will be too big for an egg carton, but that's a neat idea for smaller flowers.
Can I just put them in a tupperware container with a lid? Will the flowers get too dry and break? I am worried about making them all and then having them break and fall apart right before I need them and running out of time to make more.

Any container w/a lid - like a shirt gift box. I would not suggest tupperware as that would seal in any moisture there might still be in the flowers and they will wilt/soften