Special needs of tree seedlings?

I'm just starting my pistachio trees from seed in containers. The hope is to grow them big enough to tell which are male and female so that I ensure good cross pollination when I plant. That means I'm entirely responsible for the early needs of these of these plants. For now they are going into about four inches of organic potting soil on top of about six inches of aged, screened, mixed wood chips. After they start poking leaves above that soil, should I be applying fertilizer or giving them any other special care as I wait for them to get large enough for the ground?

Then there's the shaping issue. How tall is a good height to start this at? Can making a few strategic cuts at a very small size reduce my pruning needs in the future or would it actually make it worse? I've already committed to maintaining two rows of espalier for the front yard. I'd like to keep the pruning of full sized trees to a minimum. I've seen people here advocating no pruning, or just pruning for shape, or just pruning crossing branches, ect. How do you decide what is the appropriate level of pruning?  I think in the long run I can greatly improve the easy of harvest if I top the central leader at a young age that it will promote branching at a lower height. I accidentally topped a black cherry we've planted for shade by breaking it's central leader during transport. It spread strong branches three directions from that point. Though one branch has established dominance as the new leader, I think we're getting a better shade tree out of the experience.