If exclusively working with the 3D layer configurator, the way you have described is the designated and also the most effective one. An alternative is to apply elevation data from external files (that would also include the top/bottom elevation of your well) by using regionalization methods.
Well boundary conditions cannot be set between layers. However, there is often no reason to do so (except for local scale models), provided that the well is located in the correct geological unit (aquifer). Significant differences in the computational results of models with different depths of the well bore are typically restricted to the area very close to the well. Wide-range effects are usually negligible.