Will my federal registration of a copyright for a computer program also cover its associated user manuals?

You can register a computer program and its documentation with one application if the same party owns the copyright in the program and the documentation. If the works have been published, they must have been physically bundled together for distribution to the public and first published in an integrated unit. If the program and the documentation were published separately, or if different parties own them, each element will be considered a separate work, and you will therefore need to submit a separate application for each.