This is a little bit aside and I could be mistaken here, but I thought it was said at one point that bloodline powers don't manifest until puberty. If this is the case, how do mixed lineage families decide where a child is trained?

Partially, at least, due to physical appearance. Red hair? Virdans or Emmans. Epicanthic folds? Send them to the Ishi. Overriding self-righteousness? Must be a Tensen.

For the val'Sheem worshipping Neroth, I have a very appropriate back story for him, but the player keeps getting verbally confused on the situation.

First of all, bakground was Undisciplined Psion. The val'Sheem was born in the Pirate Isles after a val'Sheem with significant pride made a business trip to the area. After birth and notice of grey eyes, the val'Sheem refused to believe the val child was his daughter, risking embarrassment while holding onto old ways. A val'Mordane family living in the Pirate Isles that knows the mother instead accepts to adopt the child until her bloodline is absolutely determined, permitting influence of Neroth's worship. After discovery and proof, the val'Sheem father is embarrassed socially of the proof when confronted by it, citing that the meeting between the daughter and father caused her to spontaneously awaken, which was very emotional. In the aftermath, the val'Sheem daughter is instead trained by val'Sheems far closer to the Pirate Isles, which she calls home with her val'Mordane family.

Hey! It that a dig at my main, Cress val'Tensen
? I take offense, sir. Cress is not a..... um... alright. I guess it's spot-on.