Operating method for the management and for the correct alignment of a cutting unit of a cutting machine, and in particular for the accurate alignment of a cutting blade (13; 130; 230) and its relevant scoring blade (12; 120; 220; 320), method being characterized by the fact that it comprises the following steps: (s1) determining first aligning positions between (n) cutting blades and (N) scoring blades; (s2) memorizing said first aligning positions; (s3) determining, by means of calculations and as a function of said first aligning positions, at least a second aligning position between one of the (n) cutting blades (13; 130; 230) and one of the (N) scoring blades (12; 120; 220; 320) never previously aligned together; and (s4) instructing and executing said at least one second alignment between one of the (n) cutting blades (13; 130; 230) and one of the (N) scoring blades (12; 120; 220; 320) in accord with previous step (s3).