Oh... yeah, automation is definitely a good option as well but you'll have to spend some time reading up on how automation lanes work and how to wrestle with the nodes/envelopes.
Good stuff to learn but I know you are still grappling with some of the basics, Charly. I still get tripped up by automation and for something like this I don't bother.
Mind you because I haven't really spent a lot of time playing with automation envelopes (but I really should... and will soon) I'm a bit of a dullard in that department. I also for something like this I kind of prefer the noises be completely removed as opposed to just turned down. That way I can drag the audio wherever I want and know the noise is gone. In the case where the automation envelope (or the parameter you've mapped it to) is copied along with the clip the noise comes back.
However the simple way around that is to simply bounce the automation effect to the clip... but that's another thing to learn (which you should... bouncing is important to understand for many reasons).
Cheers.
PS: "Flatten" is really just a kind of "bounce" anyway that is directly related to Sonar's comping mode. It's just kind of a really fast/convenient/foolproof way to do it.