A method of controlling a series turbocharger for an engine and a control system for the same includes a boost determination module determining a first predicted boost pressure for a first position of a variable geometry turbine when a high pressure turbine bypass valve is in an open position. The boost determination module determines a second boost pressure for a second position of the variable geometry when the high pressure turbine bypass valve is in the open position. A desired boost module determines a desired boost. A comparison module determines when the desired boost signal is between the first predicted boost pressure and the second predicted boost pressure. A bypass valve control module closes the high pressure turbine bypass valve when the desired boost signal is between the first predicted boost pressure and the second predicted boost pressure.