Preheat oven according to directions for your cupcakes. Prepare cupcake batter. Line a cupcake tray with paper liners. Place one cookie at the bottom of each liner. Fill liners to 1/2 or 2/3 mark with cupcake batter and bake as long as recipe requires (usually around 15-20 minutes).
Let cupcakes cool fully. Using a small knife (I like to use a turned around, medium-sized icing tip) cut a hole into center of cupcakes. Pull apart a granola cluster and fill into center. About 1/2 cluster, dont press in too tight. Use very top of the cut-out part to close cupcake top again.
For the chocolate glaze, melt cocoa powder and margarine in a small saucepan on medium heat; put aside to cool. In a bowl stir together icing sugar, milk and vanilla. Mix in cocoa mixture. Dip cupcakes in glaze or spoon glaze over cupcakes. Sprinkle with a few remaining granola bits.