How will integration onto our existing Fan Page work?

First, you may want to learn more about the difference between Facebook Pages and NewsCloud Community Sites.

Currently, Facebook does not integrate Pages & Applications very well. So, your Fan Page will remain active. But, your new Facebook application is the ideal landing spot for your readers inside of Facebook. How then do you direct people there?

There are a few options:

1) All of your web site links to Facebook should direct people to features and stories within your application
2) You should promote your application with links to your Page and Page Fans
3) You can use the RSS feed from the Facebook application and set it to automatically import to your Fan Page notes. Visit Edit Page in Facebook, Go to Notes -> Edit, in the right sidebar click on Edit Import Settings - and put the RSS feed from your application there.

Those are the best approaches for now.