Im a little lost because I don't know the context for sure (YOUR wiring and use on the layout.)
Out of phase can cause up to twice the expected voltage (mainly why we do it, among deeper reasons ).
With many new units and their modern breakers, out of phase usually causes the new models to never turn on, breaker trips as soon as power up happens. Older ones need an actual over amp draw. (thermal, and I would ideally back a modern one with an old thermal or fuse because I trust in mechanicals more than electronics (and electronics did feed me for years) even though the electronics are lighting fast, if they happen to burn a component, they might not trip at all.
You need both commons together at the unit. And the whole system will use one common now (black for you?) Com. to outer rails and most acc. frames/com. input. (so bumping a frame to an outer rail doesn't make a short.
Each throttle gets to its own hot wire (hot(s), center rail(s) (or constant volt terminal) ...your reds?
Now, how many and spacing between wire drops (connection to track) can impact running. More drops is smoother power distribution as wire carries power better that steel track. Position of a drop(s) on a loop can vary how an individual loco runs too. Running outside last week, I needed to taylor power to my driveway grade for each loco. Some needed only 1 drop near the grade, some needed 2 to make the loop, some needed 3 drops and some would jump the track is spots with 2 or 3, those always needed just one as far away from the rollover spots as I could.
Sometimes moving a drop 1ft to the left made a huge impact.
Also of mention, some throttles vary the common, some vary the hot. But with our version of ac, they are not TRUE hot or ground. We can phase them them to match though, and need to ID them somehow, and most people can grasp the theory if presented that way. Context over syntax 
U gadda under stand, not messisarrily speaken the Duetch well, but understand it.
So phase is done on a bench and running has no business in the test. If that is ok, wire the track up now.
Running issues are distribution issues you tackle next.
