It isn't clear if you're talking about getting the app onto your device or uploading a new version into the app store. I'm assuming the latter... Sign in, click your app, and click the Upload New Version button at the top of the page.
Right now, you'll need to remove older versions before loading new ones. I don't have a whole lot of details on the way we intend this to work, but I can give you a brief overview.
Garmin Express will have an option to update apps automatically, which I believe will be on by default. If enabled, apps will automatically update on sync unless there are permissions changes, which will prompt the user to allow the changes before the update takes place. If disabled, users will simply be notified that app updates are available and then will have the choice to update.