In a saucepan, mix chocolate chips and shortening. Cook over low heat, stirring occasionally, until melted and smooth (3 to 5 minutes).
Loosen top paper cup from stack. With small brush, coat inside top cup evenly with about 1 teaspoon melted chocolate to about 1/8-inch thickness, bringing coating almost to top of cup, but not over edge. Repeat until several cups are coated. Refrigerate the cups. Shape dough into balls and arrange on baking pans. Dip a fork into flour and gently press a crisscross pattern on top of each cookie.
In a pan, mix butter or margarine and peanut butter. Cook over medium heat, stirring occasionally, until melted (about 4 to 6 minutes). Stir in sugar and press about 1/2 tablespoon filling into each chocolate cup.
Put about 1/2 teaspoon melted chocolate on top of filling and spread to cover. Freeze until firm, for about 2 hours and carefully peel off paper cups.