The Polk RM6600 is an integrated system.
As such, it was designed to work as a single unit. The sub is designed to work with those satellites and, conversly, those satellites are designed to mate with that sub. What their directions are saying is that since the optimum balance has already been determined and designed into the system, it will work best this way.
And, like a Bose Acoustimass system, it's also a bunch of tiny mains that require different rules than a normal pick-it-yourself combination of normal sized speakers. Mainly, keeping deep bass from the mains and this most likely reuires a higher cutoff point in the sub than one would normally like..
I can say, however, that you'll have no control over the sub or mains as standalone units. How this will affect your setup procedures I cannot say. You may just have to wing it.
But, if you choose to "break up the set", and try connecting the setup in the "conventional" manner, make sure you set the mains to small. Odds are they can't take any deep bass.