I usually get one template file for each of the sldprt, sldasm and slddrw's completely setup the way I want. Spending a bunch of time getting them as perfect as I can.
You will want to spent a lot of time in the Document Properties for your start templates. 2012 has a lot more granularity on Document Settings then past versions of SolidWorks.
Then I copy the template files and morph them for size for each of the rest of the templates.
Your company may not get 100% of what they want. But you should be able to get quite a bit of it to match their AutoCAD templates.