If there is one thing that you change when it comes to paragraph settings, I beg you to change the first line indent. The default setting in MS Word is 0.5″ which is way, way too deep for even a 6″x9″ trim size. A good indent is 0.25″ for smaller trim sizes and 0.3″ looks nice for larger trim sizes.
Indent or not to indent? The first paragraph at the beginning of each chapter, subheading and after a scene break can be indented, or not indented. A majority of the time, it’s not indented because if you recall, the reason we indent a paragraph is to signal to the reader that a new paragraph and thought is occurring. Since it’s the first paragraph, you’re already signaling this by either space above the paragraph, a symbol, or another break in the flow of text (subheading), so it is redundant to signal them again.
Hyphenation is another item to take into consideration. InDesign has some great control options, whereas MS Word has less, but it doesn’t hurt to adjust the hyphenation settings to make the text easier to read and more appealing.