All I need is for the player to cast a spell bringing up a messagebox that you can type a number into, and then that sets a GlobalVariable.

At the moment you cant use default CK to create message box's with text inputs. Depending on what exactly you are going for I guess you could create a message box with a %x number linked to a global variable, set 2 or more of the buttons to incriment up or down that number then the last button to accept. kinda hard work around but some modders have done well with it for example http://skyrim.nexusmods.com/mods/14819.
Maybe SKSE has a solution?

why not just have buttons with numbers 0-9 and tell them to choose twice?

1st choice = number chosen x 10
add that to the second choice and you've got yourself a 2 digit number

That would work, but it's just a horrible interface. I'd rather keep it the way it is now with limited options. I think 10 options is enough. Hopefully. We'll see.