The bar (takeup roller) in the throat of your machine needs to be a little higher and you will have to raise it more as the quilt gets rolled up on it. You will want your quilt to lightly touch the bed of the machine.
You pull the bobbin thread to the top when you start & stop if you're in the middle of the quilt somewhere. If you're off the edges--it doesn't matter. To pull it to the top--you do a needle down/needle up and use a pair of tweezers to grab it and then pull up about 5-6 inches. You can then wrap your thread tails around a pin and pin it out of the way to go back and bury them later or take a couple stitches in place and trim them all when you get ready to take the next pass. At the end of a pass or when you stop quilting a block--you again do a needle down/needle up but then you raise the presser foot and move the machine to pull up the thread again, move the machine back to the same spot and take a couple tiny stitches or cut and wrap around a pin to bury later. It will make more sense when you've got a quilt loaded and try it. I used the auto thread cutter on my first machine at the end of every pass after taking a couple stitches in place rather than pulling the bobbin thread up again. It leaves a little tiny tail on the backside but not enough to catch on anything and if using a cotton batting, it will kind of disappear into the crinkles.