As for when to model, we always draw in 3D it helps when your looking at certain construction elements, where you can cut a section line or see it in 3D view so you can determine how your going to do something, its much better to understand in 3D/Section than trying to work it out from a 2D view.
As for layers, being a small practice we usually use some of archicads standard layers i.e. external walls, Internal walls (though depending on stories we usually have a set for each storey) drainage, external works on separate layers, furniture, lighting, plumbing etc etc.
We try have a standard but some jobs are just non standard, and it depends on how your office works and the type of projects as to what a good layer combination would be.
Also to make it easier to go through the layers we always purge unwanted layers that Archicad set, especially if we have merged a site plan map from Ordnance survey as they add about 300 layers to your drawing of which probably only 50 are used for that particular site plan.
Thats how our office works at the moment, but we are trying to form a set of commonly used layers for all the projects we have done on Archicad over the last 16 years to create a template for any job, though you can agree this is quite difficult to do as no job is ever the same.
