The allocation of cross-border transmission capacities is a basic precondition for cross-border electricity trade. Insufficient transmission capacities are the factor that limits this trade and therefore they must be allocated in the economically efficient manner in order to alleviate its negative influence on the trade but along with the preservation of electric power system stability. The flow-based coordinated auctioning method introduces economic criteria for selection of requests for transmission capacities use when those requests exceed available amounts (congestion), along with a better representation of cross-border electricity transactions influence on transmission network. With the use of internet development tools, web simulator has been created, which allowed practical implementation and testing of coordinated auctioning method, especially a possibility to apply netting of counter-flows. Several sensitivity analyses and case studies have been conducted and the results that show the advantages of application of netting principle are elaborated.