apps purchased before app store; how can I get my updates through app store?

Before the App Store came along I was buying my apps in person, mostly from an Apple Store; iWork for example. A lot of those apps are now available in the App Store, but I can't get my updates through the app store. In one case, I purchased Scrivener from the developer the day before it was released in the App Store. Scrivener does not check for updates very well. Is there a way to convert, or register applications with the App Store so I can take advantage of it's updating system? It drives me nuts every time I'm in the App Store and I come across Pages, or Numbers and it doesn't say "installed".