Should I bake cookies with the oven heated from the top or the bottom?
1.
Definitely heat from the bottom but bake on the center rack. Place a thermometer inside the oven to check that the temperature is accurate--home ovens can be off by 50 degrees or more, making a huge difference for cookies. 350 degrees Fahrenheit is a good temp for chocolate chip cookies. If the cookies turned black, they simply got overbaked. They will flatten naturally as the dough gets warm in the oven, so no need to worry about that. 

2.
If perhaps your particular recipe yields slightly "puffier" cookies than you desire, you can try any of these steps:

Use whole butter only instead of margarine or shortening--butter causes cookies to spread out, while the other two cause them to keep their rounded shape.

Add a tablespoon or two of water to the recipe.

Do not omit any sugar from the recipe--the cookies will be puffier with less sugar. 

Let the dough become room temperature before baking.