Put them below the box to get an overhead shot. If you put them above the box, it will be a worm's eye view. The red dots move together, and indicate the vertical vanishing point. Next comes the dark blue dot to the third corner of the box which will make the second (light blue) vanishing point, as well as the third corner (where the green and blue lines intersect across from the light blue dot).

The closer it is from the blue dot horizontally (as compared to how close it is vertically), the closer the vanishing point will be and the further away your scene will look. This will determine where your first vanishing point is: where the green line crosses the horizon line. Next up the green dot to a side corner of the box. You can also fiddle with the position of the dots later if you're not happy with your perspective, so put them wherever for now just to get an idea of what you're looking at. The scene you end up drawing can be larger than box we're sketching out, so don't worry about size. Next move (ctrl-left mouse button) the light blue dot either above or below the horizon at the front or back corner of an imagined box/room. You can also rotate the crosshairs (alt-left mouse button) to have a slanted horizon line like the camera's tilted on its side. Where it is horizontally doesn't seem to matter much, but the vertical position is vital to place correctly now since moving it later will move the entire ruler instead of repositioning the horizon within it. The first thing you'll want to do is move (ctrl-left mouse button) the black crosshairs on your horizon line. I could not locate any tutorials on the subject so I figured I'd make one as soon as I figured it out. Paint Tool Sai 2 has perspective rulers and perspective grids, and I found the 3 point perspective ruler super confusing and unintuitive.

Paint tool sai 2 isometric ruler