On your first question as with many perm questions, the answer is it depends. When looking for material for hugel i think it's good to begin with what is freely available on site. I would probably put big logs and the bottom, sticks and brush, then soil, then mulch on top.
Guild is a word that describes a collection of plants who's specific attributes aid each other's growth when they are planted in close proximity to one another. A lot of them are structured around one main plant like a fruit tree, vegetable, or one main pollinator. Here is an example of a bee specific guild.
I think your second question was well answered by the person before me. Your first question can be better answered as "don't layer it." You want your Hugel mounds to contain lots of different things in pockets of goodness, not in even layers. Even layers can lead to the lasagna effect (which means one "layer" can turn into a sheet that repels water preventing layers below it from getting water/nutrient flows.)
You want to bury your logs (wood) with occasional clumps of manure and straw and such scattered across the mound in pockets here and there. As long as you don't do an even layer of any of these things and your wood is completely covered by the soil, you should be good. Make sure you get a cover crop planted on the mount as soon as possible after creating the mound. You can do an even layer of mulch (straw) on top, but that is a mulch to protect the cover crop and soil.
The pockets of compost/manure/etc keep it from forming a sheet of anaerobic water repellant as already explained, but the other thing they do is add diversity to the soil itself. This means some plants will really really LOVE some spots of your mound, and other plants that HATE those spots will LOVE other spots of your mound. In the end, you get soil diversity which leads to better plant diversity, which leads to an overall healthier system.
Paul talks about this in the World Domination Gardening DVD set. If you can get your hands on that, it's worth the watch. Lots of great information.