James
I actually use two templates, both of which I created myself in Pages. The first is the 'Master' template in which the book is created and edited. With A4 paper size selected, the margins are 2.54cm (top and bottom) and 2.85cm (left and right). Working in double-spaced 12-point Courier (the traditional typewriter font) this delivers a consistent average of 250 words per page. Courier is the ugliest font in the world, but it has a very significant saving grace. It is not proportionally spaced. This means that the letters sit slightly further apart than they do with the likes of Times New Roman, which makes errors much easier to spot on screen. The word count is done the traditional way because word processors' word counts are hopelessly unreliable (textually identical Word and Pages documents, I have discovered, have word counts miles apart). With 250 to the page, four pages is a thousand words. Simple.
Apart from the title page, which has its own layout within the same margins, the layout is a single paragraph indentation of 1.27cm (half an inch) and a single header, containing the title / my surname / and the current page number. I use sections to ensure that Chapter One starts on Page 1. Although there is a footer, I leave it blank. Chapter headings are centred and emboldened and each chapter ends with a hard page break. Widow and orphan prevention is disabled because that interferes with the word count. Do not justify. Left align everything except headings. I also find it very useful to bookmark each chapter.
Once the book is written and thoroughly edited (which involves printing it out and going through it multiple times with highlighters, both forwards and backwards), it is ready for the 'Trim' version.
The 'Trim' template is also A4, but changes the margins to 2.54cm (top and bottom) and 3.17cm (Left and Right), which is Word's default layout, even though I am still working in Pages. The header is no longer needed, so I leave it blank. The font is changed to single-spaced 12-point Times New Roman and the paragraph indent is reduced to 0.3cm. As before, Widows and Orphans are disabled and text is not justified. Each chapter still ends with a hard page break. The 'Trim' copy also includes 'Front Matter' pages (title page, copyright notices, dedications etc.) each separated by a hard page break. The same applies if you include 'End Matter' pages (bibliography, glossary etc.) Although the 'Master' copy has chapters beginning part way down the page, the Kindle's small screen looks better if they start right at the top.
I don't do a table of contents because Kindle does not do pages (small 'p' - not Pages). Instead, it is the electronic equivalent of a scroll and it indicates how far through you are as a percentage, and the 'go to' feature works in 'locations'. TOCs, therefore, tend to end up just as a list of chapters. There is an endless debate in the Kindle forums on the best way to do a table of contents. My own opinion is the best way is to avoid it if you can. As I only number my chapters, I don't see the need. I write novels, of course. If I were doing reference works, it would be a different matter. The 'Trim' version is, essentially, a reformat of the completed 'Master' copy.
I now save the 'Trim' version as a Word document (.doc, not .docx - Kindle doesn't like the latter). Because it is already laid out to Word's default setting, it is seamless. Kindle is set up to expect a Word document and will set its own margins and justification, so use the defaults, lest you confuse it. Resave the Word version as Html. I use Word 2008, which involves clicking 'Save as Web Page' in the file menu and ensuring that the encoding is set to Western European (Windows). I believe in Word 2010 you select 'Save as Web Page (filtered)'. When the Html version appears (it looks like a long scroll with very wide lines, feed it through Calibre (a much nicer program than Mobipocket - and it comes in a Mac version) to produce the MOBI file that you will upload to Kindle Direct Publishing. Like Mobipocket, Calibre allows you to include a cover. It is also a free dowload (just Google Calibre and you will find it).
That is complicated, I know, but it is easier to do than to read.
All the very best with your efforts. Let me know when you are published and I will buy a copy. Kindle pays the best royalties in the industry - up to 70%.