We have a new system coming shortly that will give the option to add your own templates however here are a few tips that might be useful.

The system is fairly flexible. It does not mind how source files are added to projects, you can either use the build in menus or the standard features of each ide.

I think you can drop your own templates into the std add new item commands of each ide but you can also add/record macros that do all this (and much more) for you, macros can be assigned to your own toolbar buttons, menus and/or shortcut keys. 

Vs also allows you to create your own snippets and insert/paste them into any code editor window with a single click (or two). I haven't checked if atmel studio has this feature.

Interested to hear if anyone uses all the features, I hope this helps

Thanks