Good question, I'll answer as much as I know, and maybe someone else can jump in. I find rigging really hard and complex still, but there's a couple basic principles that might help in this case.
Joint chains are inherently hierarchies. The root joint is the first one, and all subsequent joints are children of this, as each joint is a child of the one before it, or just above it in the hierarchy. If you select a joint, you're really only selecting that joint, but it influences all its children in the same way any parent-child works in maya. You can select a joint and then shift select its child and you'll get a cool double transform that can be useful when animating (I think... not sure how useful most people find it, or if it's just bad style).
If you want to move a joint on its own, there is an option though can't remember where it is... actually I think if you go into insert mode, you can move a joint without transforming its children, hit insert, or press and hold 'd' while in the move tool.
You can go skeleton > reverse chain (or something like that) to get your chain going the other way, since it's common to rig from the base of the spine up.
So, in answer to your last question, yes the way you have it, the head joint is your root, so you'll want to reverse that.
Hope that helps.