In the first rotation (360 deg) three cylinders will fire off in their appropriate sequence (1,5 and 3 for example), the other three (2, 4 and 6)in the next 360 degree rotation. For each rotation you therefore only need to inject fuel to the three cylinders that are GOING to fire so you fire off those three injectors simultaneously.
ONE of the three cylinders will be on the intake/compression cycle and draw the fuel in to be burned. The remaining fuel in the other two (yet-to-fire) intake runners can sit there and 'wait' until that cylinders intake valve opens an sucks the mixture in (has to wait a full revolution though) - but it's far too short a time for anything untoward to happen to the fuel/air mix (it ain't going any where!) and the actual amount (fuel/air ratio) won't need to change as the throttle response is far, far too long in comparison to the actual firing sequence.
The two sets of injectors are each therefore fired only ONCE per revolution (sequentially) at a time determined by the ECU which gets its timing from the crankshaft sensor and then calculates the BTDC timing depending on load/revs etc.
As you should be able to see, there is no need to fire the injectors 'individually' (i.e. at each intake/compression/firing cycle) - charging three intakes at the same time has little effect on the end result.
Compare this to a standard carb setup where the fuel/air mix is available to ALL cylinders at the same time (for a single carb setup) or for two lots of three cylinders in a dual carb setup. All the injectors do is a better job at atomising the fuel mix and placing it where it's needed rather than it having to travel convoluted intake pipe routes (just the air does in an injector setup).
Consequently your ECU should have a pulse on one of the injector drivers, then the other. If you could connect a light to both outputs you'd see them both flashing but never at the same time - just alternately. Each pulse would only appear once every TWO revolutions of the crankshaft.
If you had an oscilloscope you could check these pulses quite easily (a dual channel scope would show the pulses and their relationship i.e. no overlap).
The time period between one set of injectors firing and the second set is just 150mS at only 800rpm!!!! (i.e. as near as dammit 6 times/second). Quite how you can tell they are firing 'together' rather than individually is rather mystifying to me - you must have VERY fast eyeballs!