Oo
Hmm can u post a shot of the messyness
The only thing i can think of (and im no expert when it comes to bones) is that u are doing something like setting the wrong weightmaps to the bones so like the left arm bone effects the right arm weightmap, or your not activating all the bones, when u activate bones it will often go really funky depending on the order u activate them but once ALL the bones are activated the mesh should return back to normal.
Im sure someone else can help u more, iv never used bones really untill i got acs4 the other day so im only speaking from what iv heard on forums and the like.
James..