Best alignments are done with cable or radio data link to the Ship's INS (SINS). Position, course, and speed of the ship are then available. Height above water (flight deck height) is entered. The software in the aircraft INS resolves the "spotting angle" -- the difference between the aircraft heading and the centerline of the ship, and the alignment can complete.
Without the data link from SINS, position, course, and speed have to be estimated and manually input (flight deck personnel may hand the pilot a sheet of paper with the info, or hold up a chalkboard. The pilot can tell if the alignment is proceeding nominally if the spotting angle output settles down at a reasonable value.