In editing, many things can go askew that will cause difficulties for the person who formats and converts your book. Some of them should ideally be double checked in the last pass an author and editor make and/or passed along to the formatter, so he/she can plan for the appropriate coding to make it convert well. What sorts of things will the formatter love you for checking or letting him/her know about?
1. Use the standard page breaks instead of slapping in extra spaces or any old page break from the list. Chapter breaks should be a simple "page break", and section breaks should be "section break [next page]". Anything else has to be changed out or it will cause conversion errors.
2. Make sure your scene break is standardized to the publisher norm. Most ask for **** or * * * * with or without a blank line before and after, but check what they want. Of everything that could be wrong in a mss, this is one of the hardest to fix simply. Extra spaces, extra returns, tabs, manual line breaks, etc. are all easy fixes to make. This one? Not so much, since it has to be searched by hand and corrected by hand, in many cases.
3. Do a final search to check your chapter headers. Make sure the numbers are sequential. If you have a missing number or doubled number, renumber them before it goes to the final edit pass. If there is some reason they are meant to be non-sequential (comedy books or something similar), leave a comment in the book file about it FOR the formatter, so he/she doesn't try to correct it.
4. Do not put any of your chapter headers in all caps unless the publisher house style is to do so. Even if it looks like the prior book in your series has the headers in all caps, chances are it really isn't so. Some fonts will appear all in caps, even if some letters are lower case. In a PDF, it won't matter at all that you've put all caps on your chapter headers, but in the ePub, Mobi and other formats which have an internal TOC (table of contents), the switch in and out of all caps will be glaring and unpalatable, which means the formatter has to retype all your chapter headers.
5. Avoid using special fonts and characters without checking with the formatter first. Some font work and special graphics must be set by hand by the formatter in creation of the ePub version and subsequent conversions of the book. It's always best to let the formatter know ahead of time if you will need this type of intervention, so he/she can plan extra time into the schedule to give your book the best possible presentation. Remember, not everything that appears in the DOC or PDF will translate well through the conversions.