Hi Jason,
We have been discussing this today, this is very likely to make the list for V2 however we are still deciding on what the best way to structure the template storage will be.
In Maxdoc V1.2 there is the functionality to use the Myfolder option you can quickly repoint this to different folders or subfolders of you templates directory. This will give you some ability to structure your template layouts however its not ideal .
Thank you for you suggestions we always like to hear feedback on how the products can be improved.
Regards
CABC Support