I got four American Chestnut hybrids from a friend - planted two per container. This situation is similar to your question.
The placement of the chestnuts and the orientation of the nut matters. I want the nuts about 1 1/2 inches apart and pointed away from each other. In the other words, the point of the chestnut where the radicle comes out is pointed toward the outside of the container.
If your container is larger, then the 1 1/2 inches can be increased.
When to replant the two seedlings? I am going to do it while they are small and actively growing - which prevents a great deal of root entanglement.
Hope this helps.
The four American Chestnut hybrids were successfully repotted to two gallon root pouches. They are super healthy. I will plant them next spring of 2017, I got them in June of 2016. They are in my greenhouse right now. They were chestnuts taken from an American that sprouted from a dead stump. They were pollenated by nearby Chinese Chestnuts.
I love those seedlings as they are the first Americans in my possession. Blumsden, they were once doubles in the same container.