According to me it's a nonsense making two applications, one the linux side and one the windows side. Everything you can make from a windows point of view can be made from a linux application (you can launch regedit, installers, uninstallers, whatever you need from linux). If you're a VB guy take a look either at GAMBAS (http://gambas.sf.net) or to KBASIC (http://www.kbasic.com); you'll find a familiar IDE to develop linux applications that can accomplish your target.
