It did take some fiddling to figure out, but here’s what worked for me:
- Go to C:\Users\[me]\AppData\Roaming\Blender Foundation\Blender\2.79\scripts\startup\bl_app_templates_user
- Create a new folder, and name it whatever you want your template to be called
- Paste in a .blend file and rename it to startup.blend
Or:
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Save your blend file as startup.blend
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Zip it
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Rename the .zip to whatever you want your template to be called
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In Blender, go to File -> Application Templates -> Load Template From File
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Select the .zip
Once you have it in Blender and your template is the active one, saving your startup file or user preferences will overwrite or create preferences for that template only.