Scott
I know it is very confusing at first but it does get easier, not that I am a rigging wizard or anything.
To answer your parenting question:
To make bone(21) the child of bone(3), for instance, grab bone(21) in the PWS and drop it ONTO, (not under), bone(3). You will see that it becomes indented in the tree.
To make a whole branch become children of another bone click on the bone at the top of the branch, press 'N' and then drag the bone and drop it onto it's new parent.
To make a copy of a branch of bones select the bone at the top of the branch, press 'N', hold down 'Ctrl'. (on a PC). and drag the bone onto it's parent. An identical hierarchy of bones will appear.
It took me ages to learn those few shortcuts and the sooner you learn them the sooner you'll get around building and testing rigs. Constraining is the real art!