I use both ways, 1 or 2 holes, so I don't think that's your problem. Can you get a decent regular stitch? When the bobbin compartment is open and you "hand turn" the needle, does it pick up the stitch correctly?
Are you sure you are using the correct bobbin? My Pfaff bobbins fit, but the sewing was all messed up.
I practiced with threading, changing bobbin, regular stitching before I tried free motion quilting. But I don't remember having to do much with tension. I think the bobbin case needed one tiny screw turn. Again, make sure it's working well on the regular stitches. I put my Pfaff away and use the Brother for piecing.