Well, a few thoughts:

1) Determine which way the kid's interests lie. He's likely going to primarily learn from a single crew member, so figure out the role he's going to grow into.

2) You might adopt something like Hackmaster's protege system for his development. In Hackmaster, you designate a protege and give them XP in short training sessions, helping them develop as characters at the cost of a slow-down in your own development. Now, I'm not familiar with WH40Ks advancement system, but I think having the PCs devote a small amount of their XP to "quality time with Junior", giving Junior more XP to work with, is a good way to make sure that the choice to have a child around is impactful in the game, and help guide his development. Someone doesn't want to donate XP to Junior? No problem, but it means they're not spending much time with the kid, and going to impact their relationship with Junior.

3) Remember: This kid is the Dependent flaw made large. He's a target. He's a hostage. He's a loving child who may bond with the characters, but he might also wind up as leverage in some of the ****tier things that go on in WH40k. Consider how nasty you want things to get surrounding the child, and what your players will be comfortable with.