The purpose of the standby temperature is to prevent oozing. The standby temperature isn't normally controlled by the slicer, it's set by G10 Pnn commands in your start gcode. See http://reprap.org/wiki/G-code#G10:_Tool_Offset. I use a standby temperature of 150C when printing PLA, and in combination with some retraction in the tfree#.g file this is very effective at preventing oozing.
To set the standby temperature the same as the active temperature, in most slicers you can do something like this in your start gcode:
G10 P0 S[first_layer_termperature] R[first_layer_temperature]
G10 P1 S[first_layer_termperature] R[first_layer_temperature]
Alternatively, in your M563 commands in config.g you can declare that both tools use both heaters, then they will always both be heated to active temperature and they will both heat up at the same time.