When I have set up my Picture plane and cone of vision and station point I've read that you need to place the vanishing points 90 degrees apart and I never understood the reason behind it? Why 90 degrees?
Perspective does not demand it. The vanishing points show where parallel lines converge. It only happens to be a fact that we have very much rectangular boxes, so there often are 2 major directions of parallel lines.
Probably your guide tells how one certain standard box should be constructed and gives the needed vanishing points. Less guessing is possible only if you show the source.
If you really do the geometric perspective construction with sight lines from the station point and have it, the image plane and the object defined in 2D rectangular projections, you cannot select freely a single vanishing point, they are all fixed due the previous selections.
Think a house which isn't rectangular. If it still has bunches of parallel lines, the vanishing points are very different, than those for a rectangular house.