How would you seperate 2 channels of audio when capturing? I have 1 channel for boom and another for lav and want to seperate them.

You cannot separate them during capture, as the camcorder does not see them as discreet channels. With an XDCAM etc, they are separate/discreet, but not with HDV or DV.
So, capture, and follow the steps posted previously (duplicate track, right click to select Right/Left only).