As far as I know the Boyer system runs with what is known as a wasted spark, so basically both coils are triggered simultaneously, so you get a spark on the compression stroke and a spark on the exhaust stroke. Hence the term wasted spark.
With this system it shouldn't make any difference which way the trigger wires from the engine are connected.
The trigger wires being reverse connected does make a difference, on a box correctly wired internally then if you reverse connect the 2 trigger wires then the timing is wrong and the advance curve is messed up too.
If it starts then to check if it is fully working you have to strobe it, as the revs increase the timing should advance, if the wires are reversed then the spark timing will not advance unless the wiring inside the box is also wrong.