Yes, clearly for your needs you want to just either create your own template from scratch (starting with the blank project and modeling it after the standard novel template as much as suits you) or refine an existing template to your needs and then save it as a new template so you only have to make these adjustments once. §7.5 of the manual covers project templates and §7.5.2 specifically goes over creating your own, so if you haven’t it might be worthwhile to take a peek at that. Given that it sounds like you’re doing a lot with Compile settings as well, you may also want to look through chapter 25 for more information on the options there.
Scrivener’s separation of draft and compile text formatting is one of its key features, meant to be liberating rather than frustrating. You can use whatever font and size and styling is comfortable to you when working on the computer, even if it’s different on any given day or any given document in your project, without having to worry about how it will appear when you print. Scrivener can do all the readjustment for you when you’re ready to compile, with minimal effort on your part. The “override text and notes formatting” checkbox in the compile formatting pane gives you the power to take mismatched text throughout your novel and convert it easily to a standard formatting.
It’s equally easy to have Scrivener leave your text alone: if you prefer to compile with the same formatting as you use for working in the editor, simply don’t check the “override” option in the compile formatting pane. You can also check “compile as-is” for any or all of your documents in the “content” pane of the compile settings and this will take precedence over the “override” setting in the Formatting pane. For instance, a title page is generally set to compile as-is so the spacing formatted in the editor doesn’t get destroyed at compile, but you can choose to have other documents preserve their formatting by this means as well.
You can easily take out the titles of your documents if you don’t want to include them, and you can replace them by something standard like “Chapter (number)” during compile. To do this, ensure that the “title” box in the formatting pane of the compile settings is unchecked and that for the document types/levels you want a standard “chapter” title included you edit the “title settings” (in that pane, just below the list of document types) and set the prefix to whatever you’d like, e.g. “Chapter <$n>”. Except for documents checked to compile as-is, which will not print a title or prefix/suffix regardless of other settings, the prefix and suffix will be printed whether or not the document title is included. The <$n> variable will be replaced in the compiled document with an incremented Arabic numeral. You can view Help>Placeholder Tags List… to see all the possibilities and for further information on the variables.
You can then format the appearance of this “Chapter <$n>” title in the sample text box in the bottom of the pane, centering it, resizing it, etc. as you like. This applies whether or not you have selected to override the other text settings. You can also select specific documents to not include the prefix/suffix via the processing options tab.
The “page padding” option to the right of the “title settings” lets you put in a number of blank lines that will appear before the title (or the prefix/suffix if that’s all there is) if that title is the start of a new page. I’m not clear whether that’s what you’re attempting or if your problem with padding is that all text everywhere ends up flush with the top of the page—if it’s the latter, then it sounds like you need to adjust your page settings. Check that tab in the compile settings and either explicitly set the margin there or ensure that your project page settings (File>Page Settings) are how you want them, if you’re using that option.
Modifications you make in a project’s compile settings will be preserved in that project once you click compile; you can also hold down the option key to change the “compile” button to “save” so that you can preserve the settings and close the compile pane without compiling. To save the compile settings so that they’re available to load later (in other projects or after you’ve made changes to the settings in this project) you can use the “save…” button always visible in the bottom left of the compile pane. So the formatting preferences don’t “disappear”; they’re just compile settings, not writing preferences, so they don’t affect anything outside compile.
For text formatting in the editor, note that the main text style preferences set via Scrivener>Preferences are global and apply to all new projects. If you’re painstakingly crafting text formatting for a specific template, ensure that you’re doing so in the Project>Text Preferences pane and that the box there is checked to “override text formatting for this project.” That way your settings for new documents created in the project will remain as part of the template even if you change your global preferences later. (Any formatting you do for documents saved as part of the template will retain their formatting regardless of your main text style preferences; this is for new documents created.)
I’m not quite clear on what you’re saying about preferences for numbering; what sort of numbering and where? Also you mentioned “Format,” “Templates,” and “Presets,” and I’m not clear on what you’re referring to by all of those or how you’re seeking to use them in your project template. Presets are global and not saved as part of the project template. Document templates are explained in the manual §8.4.
I hope that helps a bit. I’m not sure I quite answered all your questions, because I don’t fully understand the difficulties you’re running into deleting elements of the pre-existing template aside from the few specific issues you mentioned. Feel free to explain if it’s still troubling you.