First and foremost, store your templates away from your installation. Anything you customize should be saved outside of the default folders – and this location should be backed up regularly (I had to say it).
Keep all templates under a single top level folder, then categorize them by adding a sub-folder.
For example, my top level folder is called Templates 2015. Inside that folder, I have sub-folder for each of the classes I teach: Advanced Part, Assembly Modeling, and so on.
The sub-folders will organize your templates and become the names of the tabs you’ll see in SOLIDWORKS under the File > New Advanced Dialog:
Stay organized and thanks for reading!
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