In short you need to have the base v1 msi and the updated v1.1 msi then run a tool to compare them and create the patch. You can do that with Wise Package Studio, but not the light version that comes with DS 6.9 I think, or you could just use the windows installer SDK tools.
This article explains upgrades and patches in detail - https://www-secure.symantec.com/connect/articles/handling-upgrades-and-patches-wise-package-studio
This is a good walkthrough on how to do it with the windows installer SDK tools - http://support.microsoft.com/kb/314131
You can probably do it directly in visual studio as well.