the skin modifier contains only the bones influencing the mesh you want to animate. you can still move the other bones - which in fact you have to do to get both meshes to animate at the same time 
with the other stuff i can't really help. sadly animation ain't my cup of tea, but in the past i got the impression that you've already done some animation stuff.
actually you have to test this out. i am just going with what a model import shows me. it could be that the script only reads which vertex is weighted to which bone, and afterwards rebuilds the skin modifier with that information. anyhow, i read somewhere that this safes processing time on engine level, and i can't imagine that a bone with no weighting information is to any use to the modifier. yes, different mesh skins can share bones.
How can you tell all that from the skeleton? I can't tell anything I can barely see the bones.
I will say I may have just answered my own question... if there are two different meshes with a skin with the neck bone, how can that work? Each one will have a 1.0 weighting of its own. That sounds like a recipe for disaster.
But then I think I unanswered my question... won't the head be required to be attached to the pelvis bone that shares the model name?
Confusing, how can 2 things have 1.0 weighting control. Or does this thing somehow accept .5 from two different meshes? I dont mind doing 1.0 to the head only or removing this bone from the body mesh but the root bone is still in question.
EDIT: I guess the vertices don't have to be painted to the bone just because it's in the skin. Right now only the root bone i shared and it has not weights on the head. But the head key frames still wont save!
if there are two different meshes with a skin with the neck bone, how can that work? Each one will have a 1.0 weighting of its own.
Yes, but they also have the same vertices where they blend together, so both meshes will still remain "glued" even when the common bone moves.
Or does this thing somehow accept .5 from two different meshes?
No, the weights being normalized, the sum must be 1 within each mesh. As I explained before, when there's a common bone, there should also be a set of common vertices (as in copy the end section of one mesh and paste it as the start section of the other one). For the joined meshes to move together when the common bones are animated, the vertices weights must be the same in each mesh.
So I should remove the head bone from the body skin and all bones from the head skin?? This is specific to NWN2 can't find it out anywhere
If so, are they allowed to share the neck bone?
Yes, the meshes are allowed to share bones (see boots and armors for example). As I understand how it works in 3ds max / NWN2, all vertices need to be influenced by at least one bone upto a maximum of three, but not all bones need to influence the mesh. The bones with no influence seem to be removed by the Expotron export process.
Ok so the neck will be shared and the root named bone although that one is not weighed. Solved my keframe problem my own mistake.
When ever I set a key frame and move the neck or head bone, it doesn't seem to "take" once I move back to that frame to watch it.
I only had this behavior in two cases:
a ) the mesh was not rigged correctly
b ) the auto key was not on (consequently, the sequence of frames between the starting position and the ending position was still).
PS also wondering if there is a quick way to edit the field in a weight table? Like anyway to select all of them, or at least a faster way to type in 1, and then advance (only enter works and then you have to click, tab, down key dont advance it).
I didn't find how to select a range of vertices. However, you can select several vertices clicking on their number in the weight table. The other way is to select the vertices globally (if for instance I want all vertices from the right foot to not be influenced by the left foot, I select the vertices for the right foot from the mesh, and set the weight using the "wrench tool").
Thank you I just figured out that last time myself.
Good way to handle a joint where two bones meet and need 50/50 split in influence:
Select left bone.
Select the vertex loop that is shared
Click .5 in the weight box
Keep everything select but click the other (right bone) now.
Click .5 in the weight box
It will be added to the list with.5 each.
For anyone following this I'd say this weighting process is about 75% done. Which means we can start talking about how we want this guy to walk right now.
I think I will make a new thread for that, as this is the end of the documenting and tutorial process and we can start talking artistically about the fatty in his own thread now, with a focus on looks and accessories.
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