Joey,
The first thing you need to consider is the size of the application. If this is a very large application, say, 100 or more VIs (not including native VIs), then I would suggest using a loader.
As I suspect it is not, then the best thing to do is to go to your top level application, choose save with options, and save it for application distribution. Then, go to the application builder and you can now build it with ALL subVIs including the native functions such as Error Handler VIs.
Good luck.
PS: You will still have to include the run time engine.