The basic cooking technique is the same for whole amaranth as for many other whole grains (e.g., barley) and grain-like seeds (e.g., quinoa): bring water to a boil, add the grain, simmer uncovered on low until the grain has reached the consistency you desire (that is the only true definition of "done" -- never be afraid to taste your food as you go!), then let cool. Even when packaging suggest soaking, I do not soak my grains and I have never had any problems. OF course, others will insist soaking is necessary. My advice, if you are concerned: try it both ways and see which you prefer.
For each part of whole amaranth, here is the proportion of water:
-- porridge consistency, 3 parts water (some liquid will remain)
-- soft texture but with distinct grains, 2 parts water
-- firm texture (pilaf), 1 part water
If the water has nearly all cooked off but you want a softer texture, add extra water and keep cooking. If you are not sure what consistency you want, err on the firmer side, and taste as you go. Note that larger batches (say, over 1/2-kilo of grain) need less water than smaller batches, so plan accordingly.
Adding salt to the water at the start is optional but I encourage it. The point of adding it early is to incorporate the salt into the grains evenly. Under-salting will mute the flavors substantially. Adding salt at the last minute will provide a burst of salt on the tongue that is not always pleasant or desired, especially if you serve the grain with some other moderately salty food.
As for fat, I don't add any because I usually serve the amaranth with something that is already fatty (like an enriched sauce). If you want to add a fat, then I would do so before the water has completely cooked off to ensure the fat coats the grains more or less evenly.
Oh, and I love using an automatic rice-cooker for my grains, as it automatically turns off when the temperature of the food rises substantially above 100 C (meaning all the water has cooked off).
You said that the dough rose but then didn't proof.
Lightly textured whole wheat bread is difficult for two reasons-
1- There isn't as much gluten.
2- The gluten that is there tends to get cut up by sharp wheat fragments.
The result is, as with all poor gluten development, that the loaves have trouble maintaining their structure, don't rise as well, and the result is the dense, tough, or doughy bread that most people think of with horror when they think of whole wheat.
There are a couple ways to deal with this problem-
1- Use very very finely ground wheat flour. If you can feel gritty shards then it will have trouble rising.
2- Add vital wheat gluten. This may be seen as cheating and is similar to the transitional recipes that you said you had success with. Many whole wheat recipes call for extra gluten.
If you don't add more gluten in some form you can make a successful boule but don't expect it to be as light and open as one made with white flour.
What you might lose in delicateness you will more than make up for in flavor and nutrition.
Best Answer
Graphics and quoted text from: Whole Grains Council
Grains, by definition, have 3 major parts: the germ, the endosperm, and the bran.
Whole grains are those that have all of the parts of the natural seed, or kernel (not including an exterior husk that is generally inedible).
To be called "Whole Grain" the product must still have all of the bran, endosperm and germ that it had when it was in the field, although it can milled, ground, cracked, natural, whatever...as long as it still has all of its parts.
This graphic shows what's lost when wheat is refined, and what's added back when it's "enriched":
Durum is just a variety of wheat. Unless it specifically says "whole wheat" or "whole grain", you can assume that it is refined.