The important thing to remember is that the only parts of this program's capabilities that are for anyone other than the author, is where you enter text and where you output all the text in book format. So book title, chapter titles, scene text, MAYBE scene titles...
The character list, location list, parts, plots, and all that, are just for you. If you don't see a use for them, don't use them. Maybe later you'll think "oh I should have used that feature to..." - or maybe you won't. So far I've never used the Plots table or tab, only actually used Parts a couple times, played with the Assistant but never in a real project, and not found much benefit to Strands. I'm sure there are other people out there who would read that and think "WHAT? How can you possibly write in this program without using THAT feature?" to every one of those.
(On the other hand, the Character Categories default to "Major" and "Minor". I have a project here with seven Character Categories, with the default ones both gone. On the same project I make heavy use of character Attributes, to code such things as species.)
I don't know what's going on with your scene list, it's quite customizable (although some of the customizations don't get saved, darnit). But look over to the right, just above the scroll bar, there's a little box with a down-arrow overlaying a rather boxy looking thing. That's where you can choose what columns appear in the list. (There are similar boxes on most other lists too.)
About inserting scenes, I use a trick that I learned many years ago while keypunching program code:
NUMBER THINGS IN INCREMENTS OF TEN!
That is, you don't number your scenes 1, 2, 3, etc. You number them 10, 20, 30, etc. This makes it much easier to insert things in the middle.
(I've asked for an option to make this the default.)
The only place I've encountered where that's a problem is if you choose to have your outputting of the book include chapter numbers. But you can just as well use chapter titles instead, and then you can title the chapter that is numbered 10 as "Chapter 1" if you really want to.