My daughter who is now 2 years old attends Catholic mass with me every other weekend and Episcopal Church with her father every other weekend. Her father and I were never married. I grew up in the Baptist Church, attended the Episcopal church for several years, and now am participating in RCIA to convert to Catholocism. My daughter was baptized in the Episcopal Church.
There are two ways that someone can be considered a Catholic. Either they are baptized Catholic or they are received into the Church. Since your daughter was already baptized she would need to be received into the Church. Normally this process would be done through the Rite of Bringing A Baptized Child Into the Church but some parishes or dioceses may have their own protocols. Your daughter would then experience the normal religious education process that all children baptized as Catholics usually receive.
If your daughter is received into the Church she would then be considered Catholic by the Church. The fact that she is unable to attend Catholic Mass when with her father would not affect her status in the Church.