After integrating a project with source control any custom templates that are used in the project won't be added to source control, this behavior is by design and allows custom templates be used across multiple projects.
If you want to add your custom templates to source control this can be done manually by adding the following folder to your source control provider:
Windows Vista, 7, 8:
C:\Documents and Settings\All Users\Application Data\Innovasys\DocumentX2013\templates
|The C:\Programdata and C:\Documents and Settings\All Users\Application Data folders are hidden by default in Windows, to access them you will need to enter the folder address manually in the address bar in Windows Explorer|
Any get latest, check out and check in operations will need to be performed manually using your source control providers client.