How can my daughter get custody of her children?

If she is in California she should ask the court for an emergency mediation and ask for a order allowing what she needs. She should hire a family law attorney.

Your inquiry is unclear. Your daughter obviously has custody if she is the mother of the children. I assume the "child custody" case is the father asking for a parenting plan that allows him time with the children. Depending on the facts of the case (has the father had ongoing contact, age of the kids, etc) the court may allow her to take the kids as long as the father gets reasonable time with them as well. The real question is whether a long term situation where the kids are gone two months at a time and constantly switching schools is in their best interest. Without the details, I can't say what a court is likely to do. Your daughter should get a lawyer as this will be a difficult situation to work out appropriately in the best interest of the children.

If dad wants to maintain regular contact, she will have to leave the kids behind. The dad has as much right to see the children as does the mother, therefore in Idaho dad will have primary custody and then she can visit when she's not working.

Seek temporary orders allowing her to obtain passports and to go with the children.