Ah, I might have misunderstood you to mean that the title was offset only after compiling (a common teething problem, as Scrivener is a little different than most of the familiar word processor style programs in that it is designed to offload pretty all formatting to the compile phase, often to the extent that formatting in the editor is completely ignored—hence an “As Is” flag to dodge all of that and just print what you typed as you typed it). If you’ve been looking for how to work with indents in the editor, try Format/Show Ruler. It should be familiar from any word processor style program, but if not it is documented in §15.4.1 (pg. 205 on) in the user manual PDF.
The most common cause of this is having a mixture of “old school” tabbed paragraphs vs. indented paragraphs. I haven’t checked in a while, but Kindles used to have issues with displaying tab characters (as is to be expected as literals tabs are by default completely ignored in HTML-based rendering, which is what all e-books use).
Best way to look into that is to track down a misbehaving paragraph in the original project, use the Format/Options/Show Invisibles command, and if you see a right-arrow prefixing the line, that’s your tab. Don’t worry about cleaning them out individually, we have a macro for that in Format/Convert/Strip Leading Tabs, that can be run on large selections of text (try Scrivenings mode to fix many documents at once).
That’s a good thing to do anyway as you really don’t want tabs for every single paragraph in this day and age since it reduces the flexibility of the document.
I’d recommend the “E-book” compile format preset as a starting point (in Compile, you can select it from the “Format As” drop-down menu). It makes a nice looking e-book and it will clean up all of the formatting in the book, as well as doing some menial grunt-work like making the first paragraph of a new section flush left instead of indented. If you want to play with the look of the output, that’s what the Formatting compile pane is for.
Anyway, as you might have noticed, you’re kind of jumping into the software at a point where most people are pretty much done with using it for the project. Scrivener is more the place where one would spend six months or years writing—and then maybe spending a few days getting everything out. By then they’ve been in the software for a long time, and although Compile is likely a new thing to learn, one is already at least versed in the philosophy of the software. Without that natural “training” period, you’re going head first into the shallow end of the pool. But—it can work, so hang in there, and the good thing is that once you’ve figured this stuff out, you’ll have cracked the hardest part of the program. The rest should be cake since part of figuring out how the compiler works is figuring out how the rest of the program is designed to work.