Oh, even better to have finished rewrites! And cheers also for having completed Nanowrimo.
All right, first let’s get back to the default settings from the Novel (with Parts) template, just so we’re starting from the same place. You can grab these by creating a new project with the Novel (with Parts) template and then opening Compile, clicking the triangle button to see the expanded options if they’re not visible, and then choosing “Save…” and giving the settings a short descriptive name (e.g., NovelwithParts). The settings are normally saved per project, but this allows you to save them externally and load them into other projects if you wish. Since you’ve changed the settings in the project you’re working on, loading these template settings will get you back to where you started, and we can modify it from there working from the same basis. So go ahead and do that, then in your completed project, open the expanded Compile pane and in the Format As drop-down menu, select these settings from the list under “My Formats”. You can close and delete the other project since we just used it to get the settings.
Now in your novel project, you should be able to follow the instructions I gave above to change your footer to add the page numbers and to change your spacing. By default, your part and chapter titles will all be included at the start of each part and chapter (as you’d expect)–basically, if you’ve followed the binder hierarchy defined in the template, it will look like the sample document included in the Novel (with Parts) template. The formatting by default is overridden in the compile, so won’t necessarily match what you’ve chosen to use in the editor–this allows you to work in a font you’re more comfortable reading on the screen, at a size easy on the eyes when writing at three am, but to compile your manuscript in a font and size better suited for print. We already changed the spacing; you can follow the same directions to change the font and just click the “A” button in the format bar of the compile pane to select your font. You’ll want to change the font for each of the rows in the type/level list so that your titles all match your text font.
Of course if you don’t want to override formatting at all, you can deselect the “override text and notes formatting” box in the formatting pane of Compile, but you’ll still want to go through and change the font for the different titles.
If you mean you made it a document instead of a folder, you can right-click the document in the binder and choose “convert to folder” (or “convert to file” if you’re going the other direction). You’ll want to make sure that the section is as the appropriate level in the binder for the part of the document it is, so use Ctrl-Cmd-Right/Left/Up/DownArrow (or drag with the mouse) to position it properly: ie, if it’s a “Part” make sure it’s the same level with the other “Part” folders, if it’s a “Chapter” make sure it’s at the same level as the other “Chapters”. Compile options are based off the type (folder, document, or document stack–ie, a document with subdocuments) and the level.
If you mean you accidentally created a document in script mode (so it initially was titled “New Scene”), you can just select it and hit Cmd-8 to switch it back to a regular document. I’m assuming it was the folder/file switch, but I’m attempting to be thorough.