When you start a new Capture when using Luffa Desktop you'll notice a floating button.
This button will float over you active windows so that you can flag Moments without returning to your Luffa window.
You can click and drag on the 3 lined hamburger menu to move the button to a convenient location on your screen. The small circle arrows button lets you cycle through the 5 main flag types.
This button has the same functionality as the built-in flag button, so use it as you would normally. You can even press and hold to do narrated flags, which will be indicated by the button turning green.