In my Insight, a common modification is to add a "MIMA" to the stock hybrid system, which is a small joystick most people attach to their shifter which gives manual control over what the motor is doing. Press up to add energy to the battery, press down to add power to the wheels. Tapping it shuts off the engine, left and right run programs (e.g. assist when you press the pedal past a certain point, regen when at low throttle, until the battery is full).
For your retrofit, it's possible to just program the system to do things automatically, or to only have a joystick for manual control, or both.