Thank you for the fast reply.
I have a project with a lot of vi's and other non-LV related files mixed in the folders. These folders are sometimes similar to each other, each folder support one kind of HW. The vi's have not the same name, that would cause conflicts in the project, but there are other files they can have the same name. (e.g History.txt for each HW type)
I think, it would be a very logical solution, that I specify the "Application.exe" as the destination for every folder for each HW in my case, and every LV-related file will be compiled into the executable, and every other file would be copied into the support directory, with the same folder structure, they had before. This could prevent the duplicated names in the support directory.
But the NI uses always flat file structure for some reason (I mean in the "Support Directory"). Probably, they have a good reason for that, but I cannot see what.
The better/easier way would to build your application without all the support files that are not need for the EXE to run (i.e. VI's, DLLs, etc).
Then, in the installer you make for the application, have all your support files (text files, etc.) be installed into the proper locations. In the installer, LV doesn't care about duplicate file names, and it is possible to copy files en mass to a location.