Sorry, haven't used it in the embroidery machine but have used it for some regular sewing /quilting projects. i finally decided that for me using a fine regular thread that matches color with my applique is almost better than the nylon.With practice yuou cxan get a really nice almost hand stitch look Other considerations 1. is easier to see what you are doing 2.it doesn't break as often 3.it won't melt if ironed 4.if using for small childrens items, the nylon could cut little fingers if part of the stitching comes undone

In addition to rachap's answer, every place the nylon breaks or has a locking stitch it leave a little end which is picky and causes irritation so wouldn't use it on a child's quilt. I prefer to use Mettler Metrolene Serging Thread, it's semitransparent
and blends well with all fabric colors. 100% polyester, so is very strong for being a 60 wt.thread.

Use a co ordinating thread to do the applique. It may seem a lot of work changing colours but in the long run it is the quickest way.Nylon thread can melt if the iron is too hot.Use a blanket / buttonhole stitch for the applique and they can be made quiet small or use a blind hem stitch.
Toodles
Anne

My advice is Do not use it. Try a variegated thread with your most prominent colours. It is available in cotton especially for quilting.

I have used it to sew Girl Scouts patches on grand daughter's vests. don't like to use it, but it does make it quicker when they show up with a lot of badges right before the final Court of Awards of the year! Otherwise, I wouldn't use it.

If you still want to use invisible thread after reading all of the comments, then I would recommend YLI brand invisible thread. It is the softest invisible thread I've ever found, and feels like a hair. I haven't found any need to change tension or any other adjustment with the YLI.
Another suggestion, if you want to have a very fine thread for applique, is the embroidery bobbin thread. It is very fine, and tends to disappear in to the fabric. I wish you luck with your endeavor!!