I use invisible thread in the top and bobbin for "invisible" machine applique. Here are some things that I have learned to keep in mind:
1- Needle size, I use size 60 needle when I use invisible thread in the top and bobbin for applique. For machine quilting, I use size 70 Quilting Needles.
2-When you wind the invisible thread on the bobbin, go really slow to avoid stretching and don't wind it full, half full is plenty, remember the thread is so fine.
3- I do adjust my bobbin tension, so that when I hold the thread it doesn't pull out too freely and it doesn't get stuck either. See how it feels now with the regular thread to get a feel for it.
4- I also adjust my upper tension lower.
Depending on what you are using it for, you may need to adjust stitch length too. Test it on a piece of the project materials and adjust as needed.
I stopped using invisible thread in the bobbin for quilting, I just use backing matching thread, but I do like it for when I machine applique as it does make a difference there IMO. Just my two cents here. Good luck.
Forgot to say, I use Sulky, but I heard good things about YLI.