Are the built-in subs in the Aperions are being fed a copy of the subwoofer signal, or are they using the left/right channel signals? If they're connected to the 990's sub output, I'd go with small and a crossover of 80Hz. If they're using the left/right signals, I'd go with either small with a 40Hz crossover or large with a 40Hz crossover and L/R+Sub (whichever sounds better).