One thing that I found works well for me when using invisible thread in the bobbin (I use YLI) is that I wind it onto a bobbin that already has some thread on it. That seems to keep it from winding too tightly and I don't wind it all the way. It is so thin that a small amount gets a decent amount on the bobbin without being full.
I have a Bernina Aurora so I can not adjust the winding speed. I just wind it and watch carefully and don't do too much. Also I adjusted my tension a bit.