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I really don't recommend using After Effects to do any audio work. I usually use Premiere for that and then import a WAV file of the audio into AE or do the work in Premiere after rendering the AE comp.
That being said, split the layer with the audio and mute the sections you don't want.
I'm sure you're probably right but I have done more "studying" on After Effects and it may be my ignorance but after Sony Vegas Pro I'm finding Premiere a painful, awful piece of software to use. Most of what i'm used to doing is using keypoints directly in the timeline and Premiere seems to be about taking long clips and assembling them rather than lots of tiny clips and then assembling them so they match audio properly. Since I use a lot of lower thirds, images, titles etc I spend all my time applying Transforms and Effects and positioning in After Effects where Premiere doesn't seem to offer me that functionality.
So my process at the moment is to take a "Master" file of all my clips created from Plural Eyes, do a very rough pick of the clips I want and export them as Quicktime AVI files and then properly edit them in After Effects.
A year from now I'm sure I'll look back on this way of working and laugh, but given where I am now the learning curve is proving way higher than it ever was with Vegas Pro and I need to get some video out there!
You just need to learn the shortcuts. PPro is an extremely productive NLE for anyone willing to take the time to learn the interface. I've used them all from D-vision, to Avid, to FC. I have even cut using the latest version of Vegas Pro and consider it OK, but not great. (can't wait to be flamed for that)
I cut my first video using magnetic powder and a razor blade in a room filled with 2" tape machines. Every system is clunky until you get the hang of it.
I'm with Rick; Premiere is a great NLE, but only if you know how to use it. It may take some time to learn it. If you're familiar with Vegas, you might do your audio cut there.
As to your workflow, I'm confused. What do you mean by
my process at the moment is to take a "Master" file of all my clips created from Plural Eyes, do a very rough pick of the clips I want and export them as Quicktime AVI files and then properly edit them in After Effects
Properly edit? Premiere is an editing tool - After Effects is not. After Effects is for doing visual effects, motion graphics, and complex color correction and color grading. Please tell me you're not using AE to cut a story together...