Windows tool subfolder issue

I am trying to create a tool to install some software. The installer looks for files in Folder B in this kind of structure: MainWorkingDirectory/FolderA/FolderB. But from what I can see, when I drag a folder into the tool, it only copies the immediate files from that folder and not any subfolders. Any workarounds?

Hi Mike, just catching up on some older posts here, but have you thought about including the resource as a zip file, and then starting off your script with unzipping the zip? That seems like it would help.