As this virtual laboratory practicum, which is a tool for mastering theoretical principles and practical skills in digital signal processing, was developed, users (mainly students) were given the possibility to parameterize harmonic signals. It includes the determination of the number of samples, sampling rate, amplitudes, initial phases, and other characteristics necessary for accurate metrological measurements. This publication presents the structure of the virtual workshop and the mathematical model underlying it, with an emphasis on aspects of analyzing the procedures for measuring the phase difference of harmonic signal models using the Discrete Fourier Transform. Particular attention is focused on the phase correction algorithm, which is aimed at improving the accuracy of measurements of the phase difference of signals. The presented methodology describes in detail the measurement process, estimation of errors arising from limited measurement time due to non-synchronization, the influence of the initial phase values of signals, and shows how the synchronization process contributes to a significant increase in the accuracy of measuring informative parameters.