An aquaplanet compset exists (F-EAMv1-AQP1), and an aquaplanet run should be able to be setup via something like:
res=ne30pg2_ne30pg2
compset=F-EAMv1-AQP1
case=${res}.${compset}
cime/scripts/create_newcase -case $case -res $res -compset $compset -v -project $wcid --handle-preexisting-dirs u -pecount S
(thanks Andrew Bradley for instructions).