The first section of the notation panel contains a little "keyboard" made of select boxes with the interval names inside.
You can click on each of them and select how you want to display that degree.
For example you can choose to display all the b5 as #4 or the 2 as 9.
Once you select a name for the interval the settings will be applied to the whole document, including the degree selectors of the chord builder and the scales generator.