Someone recently posted link to a Leah Day video showing how to work machine quilting thread ends in easily. You may be able to find the demo by searching.
Basically what she did is use a "cheater" needle -- this is a hand sewing needle that has an opening in the side so you don't have to thread through the eye. She brought bobbin thread up to the top, held both threads together, slid them into the cheater needle, then took a long stitch into the quilt sandwich -- starting near where the threads came out and looping it through other stitching. After pulling the needle out, she cut the threads near where they came out.