Populating all the fan mounts is generally a good idea. Using the top mounts as exhaust will help heat expell from your system. So, that will increase the efficiency of the Phantek cooler that you have bought.
It also helps with dust.
Just make sure you configure your fans properly.
OK, to answer your questions.. The Noctua's are AMAZING... but can be more expensive. If they are the same cost as the corsair, then get the noctua. I have noctuas on my cpu cooler and they are silent, and quiet at full speed. Your case is build around being quiet and using the top fans would add to the noise so I would recommend NOT using them unless you notice your temps are higher after getting everything built.
You really should be fine with 2x 140mm fans on the front and a single exhaust. If you want to populate all the the top fans, you would see a improvement in cooling, but keep all the exhaust fans on low so reduce noise (it will be enough airflow to keep things cool too.) Then have the intake fans on medium.
You also want to keep more air being pushed into the case than is being pulled out. This will keep positive airpressure in the case and push dust out the nooks and crannies of the case instead of sucking it in.
I currently have an antec 300 with 4x 120mm and 1x 140mm fans. 3x 120 intake. All the fans are at low and this keeps all my components very cool and quiet. Your 140's will move more air and you can probably run them at medium with less noise than my 120 antec fans. So I think you should be find with that.
thanks