We present the met determinate hodological features and new subsystem for receiving, digitizing and processing signals at the intermediate frequency of the incoherent scatter (IS) radar. The implemented method, subsystem and flexible software made it possible to avoid the influence of a number of instrumental factors on the accuracy of determining the quadrature components of the IS signal correlation function used to determine the ionospheric parameters, to adapt the digital filtering parameters, the value of the correlation delay step and the number of ordinates of the measured correlation function to IS signals from different altitudes and under different space weather conditions, to effectively test radar systems for the subsequent taking into account hardware factors and, thus, to improve the accuracy of the measured ionospheric parameters. The experimental results are presented.