Before adding whole (flaked & cracked as well) grains to your dough, the best thing you can do for them is give them a soak. It not only makes them softer to chew and helps out our good friend gluten, it also prevents them from sucking moisture from the rest of your dough.
If you're planning ahead, simply soak your grains in an equal amount of cold water overnight and when you wake up, all the water should have been absorbed and you're ready to rock in the dough making department. Now for those (ourselves included) who are more the "fly by the seat of your pants" and might be baking at the last minute, try combining equal parts of grains and water in a sauce pan. Bring it to a boil and let simmer for 5 minutes. This should give them enough juice to do their job, just make sure you let them cool down (under 100 degrees) before using so you don't harm your rising process.
The only tricky part is to remember to deduct out some of the water from your dough recipe — half to be exact. So if you used 1 cup whole grains, subtract 1/2 cup liquid from your mixture. The crowds will go wild and your "healthy" breads will be changed forever. You're welcome!