When opening a PDF presentation, SlidePilot will open two windows:
The Presenter Window, which gives you the information and control about your presentation (Clock, Timer, Slide Preview, Notes, ...)
The Presentation Window, which just shows the current slide (with optional pointer, curtain, ...)
If you have a second screen connected to you Mac, the Presenter Window opens on your primary screen and the Presentation Window on the secondary screen (a beamer or TV for example).
If you have just one screen, the Presenter Window will open on your main space and the Presentation Window will open in fullscreen mode.
If this arrangment does't fit for your purposes (or you have more than one screen connected) you can simply drag and drop the windows to the screens or spaces you want by using macOS' Mission Control.