Expanding on this a bit, if the manifest is available at compile time it's included as a resource in the executable by the RC resource compiler. You can embed a manifest into an existing executable with mt.exe. Embedding the application manifest is recommended.

If you can't embed it for some reason, then you can distribute the application manifest side-by-side with the executable by appending ".manifest" to the binary filename. In this case probably already have defensive checks for other resources not being found if a user copies just the exe, and if not can add one and exit.