All speakers should be configured as small.
It's important to set the crossover frequency to 80Hz or higher. Sometimes higher makes things sound better.
Setting the size to small really means "enable bass management". It's not an indication of the type of speakers you have. When bass management is enabled, low frequencies, the ones lower than the crossover frequency, are diverted from the speakers to the subwoofer. The subwoofer should be able to do a much better job of reproducing those low frequencies than the other speakers can.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped