Have you run the receiver's room equalization software (YPAO)?
That should help balance the outputs of your speakers -- both their volume levels and their frequency responses.
Also, before you run the calibration, make sure the center speaker is oriented so that it points up (or down) toward where your ears are located in your primary listening position. Most tweeters are directional, so if you're off-axis, they don't sound as good as when you're on-axis. If it's in an "entertainment center", make sure that the center speaker protrudes out from it, not set back in the shelf.
Marantz SR7009 avr + MM9000 amp --> Atmos 7.1.4
Fronts=NHT 2.9+AC2, FH+TM=DefTech PM1000, LCR+TM amped