How do I use the Jaffle iron to make pies?

Agreed, any pastry dough! You could use a standard pie crust dough -- for something like a chicken pot pie, a biscuit dough works really nicely. I also think using phyllo dough would be great as well for something lighter.

I think you can use just about any thick batter or any pastry dough. Many years ago, I saw a short program on the jaffle iron and the man used buttermilk biscuit dough, corn muffin batter, bread slices, and pie crust. The corn muffin batter was the most interesting because he added cooked cubed smoked turkey, cheddar cheese, and mango chutney. I think you just have to grease the jaffle insides to make sure that the finished product will release easily, which in my book means grease well with lots of butter (I've never had much success when I used oil or shortening).