You mentioned using invisible thread .... are your stitches OK when you use the same thread on both the top and bottom?
Also, are your stitches ok, if you are doing regular straight stitching? Check there ... and get it set up to stitch well in that mode first.
I don't know your machine .... you mention threading the bobbin clockwise and counter clockwise. Is that something specific to the machine? I've never heard of that before!
Ask your LQS for a private lesson. It won't likely cost you too much. They can tell you all they like, but this way you can have them guide you thru each step ... and help trouble shoot and then gain confidence with the technique to go home and master the skill!