Setting speakers to "small" tells the receiver to redirect low frequency sounds (the ones below the crossover frequency) away from those output channels to a separate subwoofer output channel.
Your subwoofer will be connected to the front Left and Right speaker channels. So far as your receiver is concerned, your front speakers are "large". They now have the ability to provide extremely low frequency sounds. It can't tell that those frequencies are actually being provided by a separate subwoofer. The crossover network built into your subwoofer itself will pick off the low frequencies for itself and pass the higher frequencies on to your actual front speakers.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped