Going through in order:
Front matter - Yes, you’ll need to put the front matter into the Draft folder at the top for now. The Mac version has a special “Front matter” option in compile that Windows doesn’t yet have, so it sounds like you’re using a version of the template that had this before we cleaned them up for Windows–sorry about that, as I know it’s just adding extra confusion! You could create a new project from the current Novel template to see how that’s set up, if you think the visual might be helpful (and you can then compare that with the compile settings for the new template)–basically, a Title Page up as the first thing under draft, and then anything else there you might also want–dedication, forward, whatever. All of that should go before the first chapter, but inside the Draft folder.
“Chapter one” - This is a prefix being added before your title. To remove it, in File > Compile click the blue arrow button to the right of Format As and then choose “Formatting” from the list on the left. Click the folder row in the table that appears, and you should see the sample text at the bottom showing “Chapter One” along with “Title”. Click the “Modify” button and then “Title Settings” and you can just delete the “Chapter <$t>” prefix that’s there. This will then give you just “Title”, which means each of your folders will have their binder title included in compile–so your “Seven”, “Nine” and so on. If you don’t want that either, deselect the “Title” checkbox in the folder row. Likewise, if you don’t want the document titles (“9th August” and so on), move down in the table to the document row and deselect the title there. If you have two document rows, one called Level 1 and one called Level 2+, just do this for the Level 2+ row. The levels indicate where the documents are in the binder hierarchy, so Level 1 will be documents immediately below the Draft folder, Level 2 will be those that are subdocuments of folders or files immediately below the Draft folder, and so on. (The plus means that all documents at level 3 and higher will use the same formatting as what you’ve set for level 2.) Since these documents are all inside your chapter folders, that makes them level 2 at least, whereas your front matter is all going to be level 1, so this allows you different formatting for those.
TOC - At the moment, this is just automatically generated; there’s no way to create your own. The TOC will be based off the page (section) breaks set in compile, so if you look in the “Separators” section, the “Page break” setting there will determine what chapters or scenes are listed in the TOC. Probably you want to have “page break” set for the text/folder separator (so that new folders–which I’m assuming your chapters are, given your description) will start on new pages, and thus will be listed in the TOC. Folder/text will probably just be “empty line” or the like; this is what divides your chapter folders from their first scene, so for instance if your chapters compile with the title, it would put the chapter title on a line, an empty line, and then start your scene text (or scene title, if you’re including titles). Text/text is what will divide your documents, and folder/folder is the divider for two folders that come next to each other. Also, any documents that have “page break before” ticked will override these settings, and they’ll also show up in the TOC.
If this is completely unclear, I’ll try to get some images up later, but I need to go help move furniture for the Christmas tree’s arrival, so I’ll peek back later and see if you’ve had any success getting things set up. You’ll be happy to know we’re working on some compile tutorial videos–Mac at the moment (although a lot of that will still be applicable to Windows), and then a slew of Windows videos are incoming.