This link goes to a short demo of creating a wireframe prototype for a web site.
http://www.urlgreyhot.com/personal/w...th_omnigraffle
The same process works for an application, using components from one of the user-interface stencils.
Since MockupScreens is an application specifically for making prototypes, it has more features related to that process that than Omnigraffle does. After a quick look at MockupScreens, though, I'd say that Omnigraffle has more options for building interaction into the prototype.