A presentation was given at Hamcom June 2013 in which the presentor allegedly asserted, "The forward and reflected waves are always in phase at the transmitter" and that was the ARRL position. A poster to one of the ham radio newsgroups questioned that statement. The short answer to the question is:
The parameters to be input to the forward-reflected calculator are the impedance looking into a transmission line in retangular coordinates, e.g. R+jX, and the characteristic impedance, Z0, of the transmission line. A voltage source of 100v at zero degrees is assumed.
The impedance looking into the transmission line is obtained from an antenna simulation program, like EZNEC, or is measured using an antenna analyzer. The Z0 of the transmission line is, of course, known and entered.
The forward-reflected wave calculator as downloaded contains the R+jX values for a G5RV used on 40m looking into the 30 ft, Z0=300 ohm tuned feeder. Ptotal is the magnitude of the real power being delivered into the transmission line. In a lossless transmission line, that would be the magnitude of power being delivered to the antenna. Ptotal can be changed by changing Vtotal, the source voltage.
On a related subject, another EXCEL file containing useful ham equation results is: