How inter-faith couples handle itI fond this article on the web. There are a lot of links and ideas you may like to check it out.
here is a snidbit from the bottom
What about children?
The arrival of children is liable to increase the level of religious tension in the family.
bullet For those denominations which practice infant baptism, the couple has to decide which church to baptize the child in, or whether to baptize the child in both churches or neither.
bullet There is the additional problem of selecting Godparents. One of their responsibilities is to act as a spiritual guardian for the child. A Godparent who is not a member of the denomination in which the child is being baptized may not be acceptable to the church.
The decision of how to handle the children's religious education is best handled early - preferably before marriage. Some couples educate:
their children in both faiths.
male children in the religion of the father, and girls in their mother's faith (or vice versa).
their first born in the father's religion, the second in the mother's faith, etc.
their children in a compromise faith. Unitarian Universalist and some other congregations often have comparative religious education courses for children.