Fire to thickest pieces
While I’m no Paul Tarlow or fused glass queen, I think you will want to use a fusing schedule for the 3 layer, as it will take longest for those pieces to heat all the way through and they will need a slower annealing period too. If you used the 2 layer, the 3 layers would not be heated thoroughly nor would they have long enough to anneal properly. I don’t think the longer firing would result in any damage to your 2 layers. Just my two cents but I’m relatively novice at firing my own kiln so may wait until Paul answers you.