The best way at the lower levels to achieve a high score is to eliminate as much of the board as possible. This ONLY matters when you are closing off the last ball. As long as one ball is open and can be easily closed off, you should leave it there for the finish. This time I'm on Level 7. I have done the hard work with trapping every atom.
Higher levels get much more difficult.
From around Level 10 on, the amount you close off becomes less important than the number of lives you have left in calculating your bonus. Around this level it becomes nearly impossible to start a stovepipe without losing a life, so you might as well plan on it. To do this you start the wall near the bottom, but with enough room to create a stovepipe. You see that you don't think any atoms will stike your bottom wall, but you actually hope that they strike your top wall. You will lost one of your lives, but then you can trap several balls in the new stovepipe.