When you create a document based on your custom document type in CMSdesk -> Content (or other type than Page (menu) item), it inherits the page template from the parent document automatically. However, you may want to choose the page template manually.
To achieve this, you will need to define a special "new page" step. It can be the same as for the Page Menu Item document type. So please go to Site Manager -> Development -> Document types -> Edit -> General tab and define a New page property like this: ~/cmsdesk/Content/newpage.aspx.