Where things sit
The script window
Two positions, in Settings › Layout.
Below the menu bar is the starting point and the safe one. The script window sits under the menu bar with room for the fill light above it. Nothing ever covers a word.
Right at the top of the screen pushes the window up to the very top row of pixels. The reading line ends up noticeably closer to the camera, which is the whole reason to do it, and your eyes look more like they are looking at the person watching.
On a MacBook with a notch, that second position puts the notch over the middle of the topmost line. That line has already been read by the time it gets there, so it costs nothing. On a Mac without a notch there is nothing to work around, and the position simply means "start at row zero".
You can move and resize the window whenever you like. Drag its background to move it, drag an edge or corner to resize. It remembers.
The reading line
The thin red line is where your eyes should be. It sits a third of the way down by default, which leaves enough text above it to see what is coming and enough below to not feel like the script is falling off the top.
Drag the small red arrow on the right edge to move it, press ⌥↑ and ⌥↓, or use the slider in Settings › Layout if you want a number. VoiceOver reads the handle as "Reading line position" and adjusts it with up and down.
While the script is paused, the line blinks slowly. Solid means the words are moving. That is the only status indicator the app has, and it is enough.
Two displays
MiniPrompter picks one display to be the one it lights. That is the built-in display if you have one, because that is where the camera is.
If you have more than one, choose in Settings › Layout or from the MiniPrompter icon in the menu bar. Two monitors of the same model look identical in a list, so there is an Identify Displays button that flashes each screen's name onto the screen itself.
The script window is separate. Drag it to any display you like and the fill light stays where it is. That sounds odd until you have the setup it is for: a Mac mini with a webcam clipped to one monitor, and the script comfortable to read on the other. The fill light belongs at the camera; the words belong where you can read them.
If you drag the script window to another display and want the fill light to follow, use the display picker. The window will not drag the fill light along by itself, because for a lot of people the whole point is keeping them apart.
Unplugging and plugging in
MiniPrompter remembers your chosen display properly, by an identifier that survives being unplugged, moved to another port and rebooted. Plug the monitor back in and the fill light goes back to it.
If that display is gone, the fill light moves to whichever one is left and stays there until the other comes back.