Editing audio from After Effects and keeping in out points

Hi, I am making a composition in After Effects, part if it is a mpg that I have set a couple of in and out points and placed onto my timeline, and have used a different part of the mpg later on in the composition. 

I am happy with the flow of it, and now I need to fix the sound. I can click on the mpg in After Effects and go to Edit > Edit in Adobe Audition and I get the whole sound along with the video on the bottom left corner. I can now run my various filters to make it sound bearable, but I don't know how I can then get this back into After Effects. If I go to save it tells me "Audio edits within a video file cannot be saved directly back into the original file" and then I have to save it as a seperate WAV. However if I import this now into After Effects it doesn't "link" to the original video and carry through my in out points meaning I would have to cut this up as well and hope I can drag it to the correct point to sync it to the video.

Sure I must be doing something wrong at the last step or how I am importing and working with it within Audition and wanted to ask for some advice.