In the flow method development, zone penetration studies are usually conducted as a part of initial screening phase. A lack of an appropriate tool can keep these studies on the level of rough estimations. The developed LabVIEW virtual instrument (VI) which processes peak signals and calculates the overlapping area and fundamental peak-related parameters was used for calculations in experiments that are modelling sample and reagent plug interaction within liquid conduits. The reliability of the predictions was initially confirmed on the artificial data set based on thirty-six files covering all the different types of cases that can be foreseen. In the continuation, volumes of model solutions, propelling flow rate, and coil length in the sequential injection analysis system, were varied by following Box-Behnken response surface design. In three examples, it is demonstrated how the VI can help us plan further experiments in the range which ensures efficient zone overlapping, economic exploitation of reagent plug and adequate dispersion. The application of the VI is not limited just to flow-based chemistry, it can also be useful in spectroscopy and chromatography. To utilize the graphical user interface, it is not necessary to have the LabVIEW program installed.