in that big of a case you’re only fitting 6?
I just checked with a piece of paper, you could easily fit 12 in there. You don’t really need a whole lot of room between each yoyo, maybe a like a cm space, if even that much. Just lay out all of your yoyos on top of the foam to plan out the design before you cut it.
As far as foam, like studio said, fabric stores should sell it. Buy the high density green foam, 2 inches thick.
To cut the wholes, I find it best to use a hunts tomato paste can (the small one). Just open up the can, cut off the top rim thing, and there you go. you have a sharp circle with a diameter slightly smaller than your average yoyo. Lubricate it with soapy water before you cut each hole so it goes in easily.
If you want you can dye the foam. It’s what I usually do, because I’m not a big fan of the green. (although 2" also comes in white)