Your manuscript should be as simple as possible. This means that you do not need to use any advanced formatting or sophisticated graphical effects. During import to the publishing software all the styles shall be converted to fit the layout of the book.

Remember - in the most cases advanced styling you do in your text editor is a lost of your precious time!

Here are some tips you can use when writing your thesis:

1. Use standard headings and styles in your word-processing program (MS Word, Open Office Write etc.), try to keep the manuscript clean and tidy.
2. Use character styles wisely, only when needed, applying appropriate styles only (bolds, italics, upper and lower script etc.).
3. Try to use specific characters for degrees, plus/minus sign, square signs etc A list of the most common special characters you can find in this article.
4. Prepare each chapter in a separate file. Name it in a way that allows to recognize it i.e. "ch_1_mythesis.docx". For the best compatibility save your manuscript (MS Word or OpenOffice files) in RTF (Rich Text Format).
5. Draw all your tables as clean as possible. You do not need to set up borders unless you need some specific ones. Avoid unnecessary columns and rows (especially empty ones!).
6. Prepare all your figures, graphs and illustrations. If you have any statisctical graphs and schemas export them into a vector-based EPS or PDF file directly from the statistics software. Avoid bitmap elements.
   You can include your figures into the manuscript or their respective descriptions only in a place where you want a figure to appear. Sometimes it's impossible to place a figure exactly in the place – in such cases the closest available place is chosen.
7. Prepare all the title and intro pages. Apply for ISBN in your country (sometimes it is a national library, or maybe your university has a range of ISBN available). Think if you need a bar code on the back cover. 

Here are Acrobat tools for proper correction in your typeset PDF file 

Add a note to a text edit
Insert text
Delete text
Delete text markups
Highlight, strikethrough, or underline text