One strand of thread is ample for hand quilting. With trapunto your first sandwich will only be the top and a high loft batting (like Hobbs polydown or wool) You do a simple outline stitch around the elements. You can also do this with your machine and water soluble thread.
Cut away the batting so only your trapunto elements have batting behind them. Then you sandwich with another batting and backing as normal. The trick about trapunto is that it requires fairly dense background quilting for the effect to truly be noticed. See if you can get your hands on the book "The Essential Quilter" by Barbara Chaney. To me this is the hand quilters bible. She explains all techniques thoroughly with exercises and lots of pictures. She covers everything from Sashiko to Trapunto to true stippling (teeny tiny micro stitching you do by hand). You can pick it up used on Amazon for basically the price of shipping.
http://www.amazon.com/The-Essential-.../dp/0715305697