This is pretty basic info, mostly for keeping your indents and making sure your text is formatted properly. These directions should work for Microsoft Word programs, or if you are using Open Office to format your text.
Save as .doc. I like to save as a totally new file name so if I mess things up to the point where I don't know how to start over, I have my original at least.
Highlight the entire thing (edit, select all is the easiest and fastest way to do this) and switch it to "text body" in the drop down menu at the top left of the program. WHILE IT IS STILL HIGHLIGHTED go into "paragraph" and change the indent to .5 or 1", whichever you want, and click "automatic." Also, while you're at it, make sure it's in the font you want and at the size you want.
You may need to go through and backspace twice (to merge with previous paragraph), then enter at the beginning of every. single. paragraph. This is tedious. And boring. And frustrating. But it is the best way to get the indents properly aligned. That I've figured out anyway.
Then go through and highlight each chapter heading and save as header 1. You can use this to create a chapter list in the front, which we will touch on later. :)
If you do it in this order, it SHOULD retain all text body paragraph indent changes you did. (You can try it with just a couple paragraphs to test, before you spent the time on it all, only to have to do it again.)
Worst case, go through and do every chapter header, then do every chapter individually.
This is the worst stuff. It sucks. It doesn't always work, but do all of that and save as .doc. That's what's worked for me. You can look at the preview of one of my things and see how it worked: Nothing Lasts Forever
It is this reason I am VERY glad I started publishing on kindle with shorter works. I learned this stuff with the shorter things. Now that I know them, it makes life a little easier.