Most people who customise a PowerPoint theme color template simply plop in new colors in the boxes without paying much attention to what they are called. It is worth doing that though to save time. When you copy a presentation with another color scheme into yours, PowerPoint will color the new presentation with specific rules. For example, text is set in “Text/Background - Dark 1”. If you colored that box with your logo accent color, you are going to spend a lot of time converting the pink text back to black every time you receive a deck from a colleague with a different template.