Build an installer including folders that aren't in project?

My VIs work in my project.  I am programmatically deploying two libraries.  When I build an application and run that the libraries don't deploy even though they are "Always Included" in the application build.  I think this is because they reside on my computer in folders and the application builder doesn't know what to do with them.  All that doesn't really matter to me because if I manually move the folders to the location where the built application resides, it works as expected and deploys the libraries.  The problem is when I want to build an installer for someone else to run on a remote computer.  I can't choose the folders with the libraries in them and where they should install to when I build the installer.  What am I expected to do?

I've had similar experiences with getting non-referenced files included in the application builder. The solution I found was to create a new folder in the destinations tab of the app builder and select all the non-referenced files to be placed there in the source file settings tab. I've only used this solution with an application builder, and have never created an installer program, but hopefully it will work for this too.
Hope this helps,
Andy

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