If the two ECU's are running in paralle, then I assume you have your standard ECU plus a piggy back ECU, but I have seen Supras with two independant Standalone ECU's but only one is used
But back to the most likely, a piggy back ECU
Basically to replace the Factory ECU with a standalone aftermarket ECU it can be expensive, and you will loose all your creature comforts (i.e. air con) so therefore we have a piggy back ECU.
This loops into your Factory ECU but the piggy back ECU looks after the cars Engine Parameters (i.e. injector cycle, mapping Tables)
There are three main parameters (maps) when tuning your car:
1.) Fuel (A/F Ratio)
2.) Cam angle *note*
3.) Ignition timing
but it still uses the functionality factory ECU to look after the creature comforts (i.e. aircon), in turn the piggy back ECU sends false signals to the factory ECU to indicate the Engine is running as normal therefore it will not trigger your car to go into limp home mode or Engine light to come on, a piggy back ecu takes signals from your sensors and modifies them to trick your ecu into reading a different value.
You Factory ECU still thinks it is running the Car but the piggy back ECU is.
Why get Piggy Back ECU
You have a greater scope to fine tune your car to its full potential over factory ECU, therefore more performance but this is only as good as the additional modifications you have done to the engine and you require extra funtionality/accuracy to tune these