Transcoding two synchronised videos

I’m using Shotcut to transcode clips out of my recorded videos into DNxHD for use in a different video editor program. Right now I have footage recorded from two separate cameras which I’d like to be synchronised with each other. Lining them up in the timeline is easy enough but I don’t know how I should output the clips I want. Can I set the in and out points on the basis of one video and then export the corresponding clips from both videos?

Edit: maybe I can set the in and out points to be the same for both tracks and then export the top video and then hide it and export the lower video?

Imgur

I made an image which maybe explains better what I’m trying to do. In the image below, I’m wanting to export clips of the two videos for the highlighted pink regions: