Although it is based on an older version of Shotcut, watch this tutorial.
One thing that is different with the version of Shotcut in that tutorial and now (version 18.10.08) is that the location of the Composite option was changed. It used to be one of the icons on the head of the video track (the section where it would say V2) in the timeline. Now you have to select the head of the 2nd video track then hit the “Properties” tab. There you will see “Blend mode” with a drop down menu. Make sure that the 2nd video track has the “Over” option selected and not “None”. After that, follow the rest of the instructions in that video and see if it works for you.
Well, I’m still working my way through it but it seems that the order in which I had masked the segments pushed those further in the timeline on the same vid track down the timeline, causing my masks to be out of sync. I tried to pull them back in line but I was missing a couple so I just deleted them and rebuilt the masked segments in the proper order.
I imagine that this wouldn’t have been an issue if I had placed each segment on it’s own vid track but I had a lot of segments to work with and vertical real estate seems to be at a premium.
I’m exporting a new copy now but I think it’s sorted.
Or you can break out the timeline, can even shove the timeline to another window (if you’re using more than one). Just grab where it says Timeline, hold & drag. Position the window wherever you would like.