Using the Mould Tool and the steps from page 4, apply the front sides of the dice.

NOTE: You'll need to flop the three to be anatomically correct in dice terms.

Ungroup the dots and the sides. Group each set of dots. Copy the dots to the clipboard ( Ctrl-C). Select the dots for one of the sides, and the side, and Arrange Shapes > Subtract Shapes (Arrange). Paste the copy back on top using Shift Ctrl V to paste the dots in the exact same place from which they were copied.

NOTE: I've moved the dots to show the results of the last action. Your dots should be directly over the holes.