Regardless of how you obtain the files (manual download or transfer from USB/CD), they be placed in the specific directory used by the IDS software : C:\Program Files\Ford Motor Company\Calibration files Third-Party & Full "Calibration Downloader" Tools
Assuming you have IDS version 120.01 or higher installed:
Downloading file directly into ids 129.09 - Diagnostic Network
With the rise of cloud-based diagnostics (ODIS for VAG, FDRS for Ford), the industry is moving toward "just-in-time" file delivery. However, for the advanced user,
Running IDS without a full calibration library usually results in Error Code 101 (Calibration File Not Found) or Error Code 113 (Checksum Mismatch). You will stare at a screen that says "Searching for Calibration..." forever, or the software will attempt (and fail) to download the file if your license is expired.