There is a config file under C:\Users\username\Documents\Visual Studio 2015\Settings\DefaultConfig.xml
.
Update: For Visual Studio 2017 and newer the path for this config file is C:\Users\Administrator\Documents\Visual Studio Dynamics 365\DynamicsDevConfig.xml
Add the DefaultModelForNewProjects
node with the name of the model to it:
<DynamicsDevConfig xmlns:i="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://schemas.microsoft.com/dynamics/2012/03/development/configuration">
...
<DefaultModelForNewProjects>NameOfModel<DefaultModelForNewProjects>
...
</DynamicsDevConfig>