Many applications have their own ink tools that you can use to write in the application’s content.
When you open an application that has its own ink tools, SMART Ink is on by default and you can write over your application.
If you want to write in the application’s content, you can turn off SMART Ink and use the application ink tools. Objects and notes on the window disappear when you turn off SMART Ink and are restored when you turn on SMART Ink.