if you use a standardized armature then there are some tools (special those from makehuman) to convert the bvh-input to match nearly the makehuman armature (there are some other too).
But if you use an armature built in your own design, you need to setup those bone-contstraints by hand. That is setting location, rotation and ik-constraints from your mesh-armature-bones to the appropriate bones of the imported bvh.
Check the samples/tutorials how to setup those bone-constraints to force the bone to use the location/rotation from another object (in this case, the animated bones from the bvh-import – first you have to scale this armature to the nearly same size !!! the armature not single bones of it!!)