Presuming you have applied the bone system to your model perfectly, you could completely animate it using bones, however this would not be Rag-Doll, simply that the regular animations, run, walk, jump and so on would be pre-animated with bones instead of hand manipulating vertexs.
The advantage with this is that you can blend animations, legs running while body turns, arms do something else, and so on. Without having to create 100's of animations for all the variations.
If you want to have Rag-Doll when your model dies, is blown up and so on, you will need to fully rig your model with bones in MED. Create some fixed animations, possibly using the bones system, or more traditional techniques. These animations would be used for all the usual animations, until the time you want to use Rag-Doll, (usually used on player death, as getting back up from the final rag-doll position will often look clumbsy and is hard to code for). Then you would need a rag-doll code, maybe in the templates, or written yourself....
In short bones are very powerful, but they are more maths than animation
and to use Rag-Doll to actually move your player around would be a task more suited to NASA
Hope thats helpful