Oy. I posted on this about a million years ago on this site and it turned into quite the discussion. Let me make this simple: Use 1" margins. Use Courier, Courier New, or Dark Courier font. Always double-space. Use a # to mark a line space or shift of scene. Never use two hard returns, because how do we know that's not a typo?
Do not space, space, space.... Use a tab to indent and use the centering command top center. In short, learn to use your word-processing program as designed.
As for word count, DeadlyAccurate is right. Word will see that as the same number of words. Remember typing class? Remember 5 characters including spaces is a "word." That's where the 250 words per page in Courier with 1" margins originates, I believe.
Word will give you a character count (with spaces). I like to take the number and divide by five. Voila! That's what I use. But remember that every typo you make in spacing, tabbing, etc., will throw that off. Not terminally, but off. Hence, use the Reveal Codes or similar command and look for problems. You can set Word's grammar-checker to check for either 1 or 2 space at the end of a sentence. I prefer 2. Use it and it will flag all the times you put only one or put three.
You would be shocked how many people put an extra space at the end of the last sentence of every paragraph. Assuming an average of 5 paragraphs per page, times 400 pages, and you have 400 extra "words" right there.
I have taken files from clients and started reformatting and fixing them. In more than one case, the manuscript became over 100 pages shorter. Formatting counts when you are counting your words.
Andy