The keywords you want to focus your SEO on should closely resemble the vocabulary of your audience. In order to come up with the proper keywords you really have to get inside the heads of the people who search for your website. What terms will people use? How do people search? Which question does your website answer? You should create a list of all search terms people could use and think of combinations and nuances within these search terms.
The limit on manual keywords could be higher. I personally wish we could input 10,000 keywords at a time, instead of 200. However, I understand the costs that Long Tail Pro has to maintain each time a new manual keyword is input. Not a deal breaker, I just wish the limit was higher. (To be fair, I don't think most keyword tools have a bulk manual option at all).