bounding box intersection is meant as an early discard of intersection pairs, so yes - first bbox and then normal collision. This can speed up the process orders of magnitude, but only if you are dealing with many meshes. If it is just about two, it wont help..
Another optimisation that is often used are convex mesh collisions (e.g. in realtime physics engines). Unfortunately Rhino has them not implemented.
If you supply more information on your problem (number of meshes in question, distribution and average vertex count, maybe we can give you better advice