1. The runtime engine is separate from the .exe and the way to include it with a distribution is to make an installer. By default, when you select the create an installer, the rte is included.
2. Paths in a built application are a little different than in a stand-alone VI. A VI is now part of an exe file. Where a path in the development mode to a VI might be c:\folder\example.vi, in a .exe it would be c:\folder\app.exe\example.vi. If you are determining the path to the external file relative to the VI's path, then that's the reason for your error message. What you'll have to do is an extra strip path function which will give you the path to the exe and if the external file is in some place relative to that, everything will work fine. To make a built app and
the development mode both work, you can code that checks and put the extra strip path inside a case statement. Using an application property node App.Kind will return either Full Development, Application Library, or Student Edition and is what I use to check the mode.