Nick –
Not sure. I have just experimented. Alibre Atom uses its own indicator rectangles for planes, and you can draw “Reference Lines” to aid construction. It is possible to toggle the former on and off but not the reference lines, I don’t think. It’s easier to delete them after use. Sometimes I use ordinary lines as construction lines and delete them afterwards.
What I don’t know is if you can leave these construction aids on the sketch so when returning to it later, e.g. if you need modify something, you don’t have to try to rebuild them or find the centres of circles.