This article describes how to work around the inability to add Bee Mobile iPack CF39 controls to toolbox of Visual Studio 2012 / 2013.
Microsoft admits that it is not possible to add custom controls which target Compact Framework v. 3.9 to Visual Studio toolbox here:
https://msdn.microsoft.com/en-us/library/hh300132.aspx (see “Application Development: Managed code and designer” section) and advices to add a control manually in code.