If the top thread is having issues on the back of the quilt, it is probably the bobbin tension.
If the bobbin thread is having issues on the top of the quilt, it is probably the top thread tension.
One things to remember is that if you change the top tension, you may have to change the bobbin tension.
If you google adjusting the tension on a midarm or longarm you should get quite a few websites to read from. I really hate to change the bobbin tension, but sometimes you have to. I would start with the top tension. I hope this makes sense.
Good luck!