I always take mine apart as well and glue them back together so I know each of the layers are fastened together. I also always take out the plastic bits in the center so they will lie a little flatter, but that is personal preference
. As for the clips, I use all different kinds to attach the flowers to depending on what I am using them for.
ETA - Do you think you might have glued or sewn them a little too far out? Sometimes the petals will 'fluff' up a little better when you use a little less glue and keep it more towards just the center of the flower - other times the flowers themselves just don't work as well on headbands, you could try doubling up on the petals to make a 'fuller' look. Sometimes I use 1 1/2 flowers on my flower headbands so they are a little fuller. Just some ideas - HTH!