1. First of all, use very few candles. In Gianna's L1 Atrium candles were used at the Prayer Table each week and for any seasonal celebrations like Christmas, Easter, and Pentecost. She also used candles for the materials which included a proclamation of the Paschal Mystery. In L1 that includes the following: the Model Altar, the Baptism area, the Cenacle, and the City of Jerusalem. Gianna did not light a candle each time she proclaimed Scripture to the children. Thus, I would recommend removing any other battery operated candles and having them just in these five areas. You will also want a set of them for celebrations so each child can receive one.
2. At the Prayer Table place a glass vigil containing a battery operated candle inside of it. When introducing the Prayer Table to the children show them how to turn on the candle and invite them to do so for themselves when they come individually to the Prayer Table for a personal time of prayer during the Atrium session.
3. Instead of placing the battery operated candles out in the rest of the environment (Model Altar, Baptism, Cenacle, City of Jerusalem), place, instead, an empty glass vigil. When a child comes to one of these areas to work the lighting of the candle provides an opportunity for the adult to come, review, and invite to prayer. In order to not lose these opportunities I would recommend having just the glass vigil(s) out for the child to place and then have the battery operated candles in a basket accessible only to the adult. When the child asks for candles to be lit the adult brings one or two candles as needed, reviews the material, turns the candles on, places them in the glass vigils, and invites to prayer. When the time of listening and speaking with God has ended, the child may "extinguish" the candles and then the adult will return them to the basket. As with real candles, the adult remains with the child until the candles have been "extinguished."
4. In order to maintain the reverence real candles elicit, I would also recommend placing the battery operated candles into glass vigils when handing candles to children for celebrations. This would include the Christmas and Easter celebrations. If you do a large group celebration for the first moment of Baptism I would recommend placing that "lit" candle in its vigil in front of each child just as we would do with real candles after having informed the children that if they choose to touch the candles or put their hand near them we will place them on the Baptism area.