How to change to color or other setting of an existing tool on the toolbar.
Tap the tool and before making an annotation, change the settings in the menu on the upper right. Then make an annotation. This will change the tool's default settings and save the setting you chose.
If you change the settings after making an annotation, the app views the change as specific to the annotation, and not the tool, so the change won't be permanent.
Look here to learn how to add custom tools to the toolbar.