In the colour options page you get to pick
- The stylesheet.
- The colours of each element individually
- Add custom CSS.
- You have the option to disable rounded corners in sidebar.
Here is the priority order for the above three
Custom CSS > Coulor picker > stylesheet.
That means Colour picker overrides the styles set by stylesheet and Custom CSS overrides the styles set by colour picker.
Note: Make sure you check rewrite custom-styles.css box when ever you update colours or layout. This will overwrite any manual edits to custom-styles.css