Preheat the oven to 425°F. Line 2 baking sheets with parchment and set aside.
Combine the multigrains flour and all purpose flours in a small bowl and set aside.
Place the water, butter and salt in a medium saucepan and bring to a rolling boil over medium high heat. Remove from the heat and add the flours all at once. Stir vigorously until well combined. Return to the heat and cook, stirring constantly, until the dough forms a rough ball, about 15 to 30 seconds.
Remove the pan from the heat and transfer the contents to a mixing bowl. Let the mixture cool for 5 to 10 minutes, or until a thermometer inserted into the center reads 140°F. You can speed the process along by stirring or gently beating the pastry for a minute or so. Beat in the eggs one at a time. The first egg should be fully incorporated before the second is added. The mixture will seems slippery at first, but will smooth out as more eggs are added. Beat for 2 minutes after adding the last egg.
Drop the dough by heaping tablespoons or use a cookie scoop onto the prepared baking sheet;. The mounds of dough will be approximately golf-ball sized. Leave a couple of inches between the balls of dough, as they'll expand quite a bit in the oven.
6. Bake the puffs for 8 minutes at 425°F. Don't open the oven door during the bake. After 8 minutes, reduce the oven temperature to 375°F, and bake for an additional 20 minutes, or until the puffs are golden brown. Remove the puffs from the oven and, using a sharp paring knife, make a small slice near the top of each, to let the steam out. Return the puffs to the oven. Turn the oven off, prop the oven door open slightly, and let the puffs cool inside for 30 minutes. Transfer to a rack to cool completely.
For cream puffs, fill each puff with pastry cream and top with chocolate ganache. For profiteroles, fill each puff with ice cream and top with chocolate ganache or sauce. For éclairs, pipe the unbaked dough into 4" long strips onto the parchment paper, bake for 15 minutes, reduce the heat and bake for 15 more minutes. Cool and fill as directed.