Preheat oven to 350° and line a muffin tin with 12 cupcake liners. In a large bowl, mix cake mix with canned sweet potato, cinnamon, and nutmeg until well combined.
Make crust: In a large bowl, combine graham cracker crumbs, butter, sugar, and salt in a small bowl. Press about 1 tablespoon of mixture into bottom of each cupcake liner.
Scoop batter on top of crusts, filling 3/4 full.
Bake until cupcakes are golden and a toothpick inserted in middle of a cupcake comes out clean, about 22 minutes. Let cool completely.
Meanwhile, make marshmallow frosting: In a large bowl, beat together butter and marshmallow crème until combined. Add powdered sugar, vanilla, and salt and beat until smooth. Transfer to a piping bag fitted with a large closed star tip and pipe onto cooled cupcakes.