I am surprised so many people have a hard time with the invisible thread and say they are never going to use it again. I have used it for years...either the YLI or Sew Art...it is a very fine nylon...about the thickness of a strand of hair...very soft, not poky. I have used it both for machine applique and for machine quilting. My biggest problem with it isn't the thread itself but something called the "Bernina Glitch"...every once in awhile...maybe a few times while quilting a quilt the stitch stops sewing...it doesn't break...and after a bit it does get going again...hard to explain unless you have a Bernina and have also experienced it...I just take those areas out and re-quilt them. But it is very minimal and doesn't really bother me.
Sometimes I like to use the invisible for applique, as I don't want any thread color showing. I will usually use a smaller zigzag and almost all the time use the smoke color as it blends in better. Smoke works best on all colors except pastels. The clear can be too shiny on any mid to darker colors.
I use a size 10 microtex sharp needle , and use a thread stand to hold the thread, not having it come right off my machine. If you don't have a thread stand, you can use a small jar to hold the thread, and tape a safety pin to the back of machine to thread the thread through before it goes through the threading of your machine. I only use the invisible thread in the top, and cotton thread in the bottom, and slightly loosen the tension.