When your layout designer begins setting up your book, he’ll first move through it to identify each distinct structural element. Under the hood, he’ll designate chapter titles as distinct from the paragraphs that follow, he’ll designate lists from block quotes; and will generally define every different piece of your book so that he can efficiently style like elements all at once, and create a harmonious whole.
If your designer is using software like InDesign, he will have robust tools that give him a lot of control over how all these elements look—once he’s identified those elements as such. So that identification is extremely critical. As your manuscript moves nearer and nearer to a definitive ‘final’ version, you’ll want to point your attention at things that will make it easy for your designer to IDENTIFY each element. However, you can safely resist the urge to STYLE them.
For example, you may be tempted to set up a title and half-title page for yourself, taking a lot of care to position your text so it looks as close to a printed piece as possible. Or you may want improve the look of your chapter titles by bolding them, centering them, or even placing a few extra carriage returns before the first line of that chapter. Most designers will undo all that hard work immediately, because technical styling is handled differently within their toolsets.
If your work includes a Table of Contents, you can simply ask the designer to add one rather than adding one yourself—your text will flow differently than it did in your source manuscript, and your page numbers will shift as well. That’s why page numbering and running heads are not super critical to the manuscript, either.
Now, if you’ve already got a heavily-formatted and styled manuscript, that doesn’t mean you’ll necessarily encounter problems, After all, all that styling probably does an awesome job at helping the designer identify each element—and he’s probably got methods in place to help him transform your work. However, if your manuscript is fairly plain (but clear), you can absolutely spare yourself the time and effort of making it beautiful before handing it off to a designer.