A desktop-to-device installation installs a product to the end user’s desktop computer first. (For this installation, you can configure it to be a single, compressed setup.exe file that contains all of the necessary files.) The installation launches the Application Manager or uses either Windows Mobile Device Center or ActiveSync to install the mobile device product onto the Windows Mobile device when it is connected with the desktop computer. Is this the type of installation that you would like to create?
If so, you can create a Basic MSI project. In this project, use the Mobile Devices view (in the View List, under Application Data, click Mobile Devices) to add support for one or more mobile device installations to your project.
