Is the pie crust supposed to be pre-baked before filling with the mac & cheese?

Hi-I've done it both ways and either way works fine. If you like a crisper crust, pre-baking helps with that, but then you have to be careful to cover the rim of the crust when you bake it the second time so it doesn't burn.

I tend to fill the crust unbaked just because it's quicker and easier.

Enjoy!

Nope. It looks like vrunka fills the crust raw. I'm sure you could par-bake it if you'd prefer, but make sure to watch that the edges don't over-cook.