You are using a thread net on a cone, right? Typically the cone is placed behind the sewing machine (I place mine in a small jar, but you can use a cone holder too), not on a spool pin, and the thread comes up through the center of the net. The cone is placed even with the bed of the machine; it is not placed on top of the machine.
If you are using a thread net on a regular spool of thread, I don't know; I have never used one that way.
In terms of whether you use a horizontal or vertical spool pin for spools of thread, it really depends on how the spool is wound. U.S. made spools of thread typically should be placed on a vertical pin. European brands of thread are wound differently, and these are the ones that feed better when they are mounted on a horizontal pin. That is why a lot of the newer sewing machines give you the option. However, I have to say I have used European brands of thread on a vertical pin on my Bernina 1230 without problems. It may depend on the specific application; I don't do anything really fancy with my machine.