Not a silly question at all. I just learned from trial and error. I use the single prong alligator clips for my hair bows, but just recently I have started using the snap clips (not sure if that is what they are really called) for my flowers. They are the metal ones that you have to bend down to open and bend up to close. They can still be added to the interchangable headbands and they sit so nice and flat on the headbands and just in the hair (this is just my opinion). I have a 3 year old daughter and I hated when the alligator clip would make the one side of the flower stick up. HTH!
With the snap clips I just hot glue on, but if I do the alligator clips I like the top (what is going to be adhered to the flower), glue the flower onto the clip, do a few stitches through the flower and the alligator clip, and then cover the rest of the clip with the ribbon. Hope that makes sense. Sometimes it is impossible depending on how thick your flower is and in that case would just hot glue.