You will have to re-pull the bobbin thread each time you start and stop.
You should be able to pull up the bobbin thread without removing the bobbin case. It's the needle down/up function that will pull the thread up through the quilt layers.
I pull out a length of "top" thread through the needle, hold it, and do the needle down/up function. You should see a short piece of thread. I use tweezers to grab that piece of bobbin thread and pull out about 4-5 inches. Then start sewing (or machine embroidery).
I do straighten the bobbin thread under the foot as it is usually over the foot after pulling.
Another tip.
Check to see what setting the auto cut function is set on. You may or may not have this feature. You may have to lengthen the setting or turn it off. The default setting may be too short.
Have you checked to make sure you have the latest update (not upgrade) for your machine? Each update is listed on the BL site and tells you about the feature it involves. Hope that helps!