I always look at how the finished product will be assembled. For example, imagine a mecanum wheel(I'm partial to 357's, but thats just me
). It would make sense to me to make the roller and all of the bearings inside of it a single assembly, mostly because that is the way it is when it is attached to the final hub, which would be an assembly all in it's own once bushings and axles are attached. However, for a product such as an AndyMark Stackerbox, I would simply throw everything together in a single assembly because there are no noticeable pieces that would need to be pre-assembled before the final product.
Hope that was of some help.