Q: Do we have to program the VFD to match only half the flow signal once we turn on second pump?
A: No. The flow should be measured at a point common to the discharge of all the pumps... 1 setpoint (adjustable), 1 feedback. The single (adjustable) setpoint and feedback should be common to all the VFD's.
You mentioned 2 duty and 1 standby pump, all of the same HP. I would suggest that the 2 duty pumps be identical and the standby pump sized to handle the load of both the duty pumps. This would give you true backup.
A simple control scenario would be to parallel a 0-10vdc feedback (flow) signal to all the VFD's. A simple lead/lag switch could be incorporated into the control circuit to select which of the 2 duty pumps would start first. Using a programmable VFD, I prefer ABB, you could program the lead drive to turn on the lag drive based on a frequency that represented a fully loaded pump. The lag drive would then start and both drives would adjust to the common feedback signal. Inversely, as the load diminished, the lead pump could shut off the lag pump at a pre-selected frequency. In the event of duty pump failure, the standby pump could be started, OR used as the primary pumping source. This can all be accomplished without the use of external logic controllers. I would be happy to provide a list of the variables and their settings.