Hi, I have the following questions below.
Hi Thomas are you using PlusSpec, PlusArchitect or PlusDesignBuild? I have responded as if you are using PlusDesignBuild.
When building a wall frame onsite or prefabricated wall frames, they always come with the bottom plate as continuous (so the carpenters can carry and lift the wall into place). Therefore, it is allowed for in the BOQ and estimate. I assume you have created scenes using the :scene-gen: scene-generation tool? Frames are associated with a SketchUp Tag (Layer), so you can turn them off, and that is why you don’t see it when creating floor plans. You may, however, see it in the section cut. We have received several questions about this, and we are seriously considering adding an option to cut the base/bottom wall plate yet still have it quantified. Can you tell me when you see it and if turning the Tag layer off will solve your issue?
The footing tool has rebar embedded ( as footings usually require more detail than slabs), and it also quantifies. As far as rebar in your concrete, I use the Slab surface material, and I created a semi-transparent material so it can be seen and quantified in the Bill of Quantities, purchase orders and estimate.
If there are double layers of rebar specified by the engineer, I will use a recipe.
3. How do I use individual bracket types and fasteners, both for sill to foundation hardware as well as joist hangers and other framing hardware?I use a recipe for fasteners and similar items EG: I associate concrete nails in a recipe as 1 Nail every 2’ of a wood frame wall. You will see an example in the tutorial video in the orange question mark at the top of the estimation tool.
As far as joist hangers, you will notice
Using recipes is the key to accurately quantifying anything, including labour or ancillary items. I am happy for any further feedback or improvement suggestions if you have any. 
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Regards Andrew