I've done both with decent results, but I remember a few times where the only way I could get things to work was to draw them by hand in layout. If you set up keyboard shortcuts for "draw bone" and "draw child bone" you can work pretty fast.
The way I approach skeletal animations for sw3d now is just to assume things are going to get tricky, and keep it as simple as possible. I do forward kinematic animation only while I'm testing the rig to make sure things will work, and often this is more than enough to finish the job.
For setting up characters with complex bone networks, modeler with skelegons is really the only way to go.. You make the bone, set the weight maps for it, etc.. Then you can just keep bringing it into Layout and convert the skelegons to bones and all the weight maps pre-set.
I've been using the import/export rig feature to re-use a bone setup that has worked well for me. There's a few steps after converting from skelegons that I've found pretty time consuming, and also some unpredictable results (although I think that's partly down to me learning how to set up bones for W3D)