The easiest way to make sure that your changes are reflected in the project is to always have the project open when you make your edits. Basically, always start with the project window open, and open all VIs from within the project. I know it takes some getting used to, but I think that it will prove to be useful.
As far as the error when building an executable, I'm working on having better error reporting. However, this problem shouldn't come up too much as long as the project is open when making all of your edits or name changes.
As far as the installer issue, the installer should preserve the hierarchy of the build output. So by including the build specification, the data directory and other directories created as specified by the build specification should automatically appear on the installed system. The only catch is if you create a folder that goes beyond the root level of the MSI directories listed. Other than that, the hierarchy should be preserved.
How is your build specification configured? Perhaps there's just a misconfiguration that is causing the installer to dump all the files in to one directory.