Quote: "The problem is, limb numbers with the objects and the skeleton doesnt match"
You have to set them up seperately, sorry...
The only quick way to do this would be to use the same skeleton in your animation editor (3dsMax / Fragmotion or whatever) and skin the different characters / objects to the same fully animated skeleton then export.
If you are using Max then there's a fully animated biped made for FPS characters somewhere (a quick search should flag it up) and there's one for Milkshape and Fragmotion too I think!