it might be simpler to live with the extra audio.
how much is it?
when you open the clips from the browser into the viewer, do you have split in /outs?
if NOT, and if the in/outs reflect the picture element, then you could open clips from border into viewer, then edit into timeline.
i think the quickest approach is to keep doing what you are doing.
actually the quickest approach is to use Sync n Link.
XML software that wil sync your clips and trim them to length
but it's a bit pricey.
nick