First, you should be sure your app is installed in the WICED-SDK/apps directory. This will keep things simple. If you have, then you should simply be able to move the application and place it in the same directory under WICED for Windows, then compile using a target.
For example, if your app is WICED-SDK/apps/myapp, then you create a target (in the right pane of Eclipse) called
myapp-BCM9WCDPLUS114 download run
If your application modifies any of the WICED files themselves, you'll have a tougher time though. So, a good starting point is to make sure you isolate your entire application in one app directory, and assure there are no modifications to WICED itself.
Also, the platform file (BCM...) will depend upon your platform.