This question is just to broad answer usefully because it's hard to tell exactly what you are asking.
My general advice: use parapgraph styles, table styles and character styles. Don't use extras returns to add space between paragraphs; dont' use soft returns and tabs to create paragraph indents. And don't use a lot of different fonts.
If you have specifc questions as you go along, post here. There are lots of experienced people who will be happy to help.
Do a Google Image search and you will find a lot of thumbnails. If you can look at previous ones for the company you are designing one for, that is a good place to begin. I assume you have spoken to them about budget, which helps determine if the whole is in color or not, just key pages with graphs (if needed), cover stock + full color, etc.
There is really nothing special about an annual report.
Take care, Mike