I was planning on just using the one gate valve on my full siphon drain. Also if to take the 90° off of my full siphon line do I still need it to be so close to the bottom? Or is that one of those things I will have to feel out and adjust through the testing process
If you take off the bend, you will want to be as close to the bottom as you can to avoid creating the vortex above the drain and sucking air. Really just need the bulkhead by itself. With your shallow box, I am actually not sure you can accomplish this you might have to have the 180 degree bend. Since you are not gluing the plumbing in, you can easily experiment.
The only thing to worry about with plumbing is that your full-siphon is running before any water creeps into the open channel.
Don't forget about the hose coming out of the sealed top of the open channel that is positioned just above the running water line so that any rise in the water level will make the open channel go full siphon by blocking off the air to the hose. Most people forget or just leave this out and this negates the benefits of the Bean system.