In a small bowl combine 1 cup warm water with yeast and sugar, stir. (It's supposed to get "frothy" but mine didn't, it did have some 2-D tar-pit-like action going on though: white circles growing in diameter and shrinking again).
Rinse quinoa (I just filled a bowl with water and strained it twice).
In a large bowl mix salt, whole wheat and bread (all-purpose) flours, and quinoa.
Add yeast, sugar, and water (from step #1, for those of you who confuse easily) to the large bowl as well.
Mix with your (clean) hands, Add the second cup of warm water ONLY as needed (I only used 2/3 of the second cup of water). Mix until moist dough has formed.
Knead on a floured surface (I washed my hands at this point, then put liberal amounts of flour on them) for about 5 minutes
Put the dough (it will still be sticky) into a different large bowl that has been coated with the oil (you can use other oils, I just like sesame). Cover with a dish towel, do not use cling wrap.
The dough should be fine on the counter but I slightly warmed my oven (140F) and just left it there for two hours. If your oven doesn't go that low, like mine, just set it at the lowest temp and leave it on for a couple minutes, make sure to turn it off before it gets too warm. 'Too warm' means uncomfortable for you to have your hand in the oven. Having a digital temp helps. You can use less time, but my dough took those two hours to rise, it more than doubled in size.
When the dough is done rising, knead for a minute or two. It will noticeably shrink, don't freak out.
Lightly flour the bottom of the pan (I used a cookie sheet) you'll be baking your bread in. Make your dough into the shape you want, you can make a single loaf, multiple loaves, or rolls. I made large two leaf shaped loaves, and rolled out a small chunk of each loaf into a thin, doughy string (about the circumference of a pencil, like Play-Doh) and wound it over the top of my loaves, yes it did flatten when i cooked it, but you could still see it and it was pretty =)
Add the rye flakes or oats on top, again this is optional.
Bake at 400F for 20-30 minutes (I baked mine for 20, because I hate when bread is so hard it scrapes your mouth up).