Which settings do you mean specifically? You should be able to set everything in application.conf (setting DTAPMode to "DEVELOPMENT" or "TESTING" also works btw)
See an example containing all possible settings here
From the settings file:
# Sets the minimum number of objects allowed in the pool before the evictor
# thread (if active) spawns new objects. Note that no objects are created
# when numActive + numIdle >= maxActive. This setting has no effect if
# the idle object evictor is disabled (i.e. if timeBetweenEvictionRunsMillis <= 0).
# Defaults to 0
#ConnectionPoolingMinIdle = 0
# Sets the cap on the number of "idle" instances in the pool.
# Defaults to 20
#ConnectionPoolingMaxIdle = 20
# Sets the cap on the total number of active instances from the pool.
#
# Defaults to 50
#ConnectionPoolingMaxActive = 50
# When the maximum number of "active" objects has been reached, the
# pool is said to be 'exhausted'. The "when exhausted" action used
# by the Connection Bus is WHEN_EXHAUSTED_BLOCK
To answer your other question, you can use both. The modeler settings will be read first, then overwritten by the application.conf values.