So today I was talking with my sewing buddy who IMHO is the queen of applique how she does it. She said many times she just layers and fuses but with a detailed pattern I was working on she gave me the steps she follows:
Tape the actual pattern (finished size) to a light box
Tape background over pattern.
Lay pressing sheet on top of background fabric
Lay pieces on top of pressing sheet that is over the pattern
Fuse
Sew.
She said depending on how many layers to an actual applique piece, you may have to "layer" more than once.
I may have missed a step or two but this is her method and the proceedure I was trying to figure out.