Increasingly, I’m getting a sense that a good work methodology is to keep each clip/shot in a separate video track until all of the filtering, etc. is completed. It seems that each scene (one or more clips) is carried on the scene video (comprised of all of the subordinate clips). The scene audio track is then added and (edited, timed, etc.) as appropriate. Does this sound reasonable?
(A quick bio note: believe it or not, I have a BA from Temple Univ.‘s Radio, Television, Film Dept. (now IIRC School of Communications). That was around the time Nixon was on the way out (i.e., not recently). I’m trying to piece together whatever I learned by, at the time, splicing 8 and 16 mm film and editing open-reel video tape. FWIW, much of my work was inspired by Ernie Kovacks’ TV work - Nairobi Trio excepted - Google same. And then I got involved in computers; the visual media, thereby, losing a potentially great artist. 
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Sounds like an odd way to me. If it works better for you that way that’s fine. 
Have you been through the tutorials? https://www.shotcut.org/tutorials/
AFAIK, the tutorials cover individual actions (editing, transitions, muting audio, etc.) but don’t suggest an overall production methodology. To be fair, “Movie Making 101” is outside of the scope of the tutorials. But some suggestions about how best to use Shotcut to assemble a complex (multiple shots leading to multiple scenes) video would helpful.
When I went looking for a video editor, some product descriptions said things like “we support (complicated stuff” while others said “no more doing (complicated stuff)”. Obviously I’m challenged by more than one “how-to”, but Shotcut certainly doesn’t leave me feeling in over my head.
(FWIW one very good way to learn something about assembling a full video of any sort is to watch YouTube videos. The list of “what not to do” is …um… not short.)
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