Using KindleGen on the command line is for generating your own books from existing files - Scrivener will handle all of that for you. All you need to do is tell Scrivener where KindleGen is. So, make sure the KindleGen folder is stored somewhere you aren’t likely to trash it any time soon (I always place it in the Applications folder). Then, in Scrivener, go to File > Compile, make sure “All Options” is selected and “Kindle eBook (.mobi)” is selected next to “Compile For” at the bottom. Then, click on “KindleGen” at the bottom of the list in the left if necessary (actually, you shouldn’t need to do this if you haven’t set KindleGen in Scrivener yet - the list on the left should be disabled and the “KindleGen” pane should already be selected). You should see a pane telling you to “Choose KindleGen Path”. Click on the “Choose…” button and select the kindlegen file in the KindleGen folder you downloaded.
That will tell Scrivener where KindleGen is, and after that you’ll be able to compile to the Kindle format directly - when you compile, internally Scrivener will put together all the necessary files and call kindlegen on the command line to build the .mobi file, but you don’t have to worry about any of that. You only need to tell Scrivener where kindlegen is once, unless you move or delete the kindlegen file.