Important to trim unused bits for export

Perhaps an unclear subject line, but I find this difficult to describe. I have a multicam clip of about 90 minutes that I am editing. I actually have a copy of that same multicam clip right above it. I do this because I often crop and have one angle on that upper clip lie on top of the lower clip. It's a class, and I'll have the teacher in a small box in one corner of the main frame, which shows the students working. I don't do this throughout the entire 90 minutes, but here and there totalling maybe about half the time. I will eventually export this for uploading to YouTube and DVD and maybe eventually some other format (haven't figured that out yet). My question is, do I need to go through this project and cut out the bits of the clip (replace them with blank space) where I am not embedding one frame in another? Will this help in the export process, or somehow make it a better quality product? Kind of a hassle, but if it's worth it . . .

So, you have a Picture-In-Picture effect, and you want to hide it for some exports, and not for others?  Am I understanding that correctly?  That is easy.
Select all of the upper clips (the smaller ones you want to hide), assign them a video/audio Role.  When exporting, in the Settigs section of the export window, set "Roles as" to "Roles as multitrack QuickTime".  You can then decide which Roles to include or exclude.
Or, you can select all of those clips and use the shortcut "V" to mute them, then export.
Or, you can Duplicate the Project, and delete the unwanted clips, then export.

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