The best way to handle ends with a sit-down longarm is to start and stop stitching off the quilt somewhere... sides or top or bottom margins so the ends will be covered by the binding. Or, failing that, you can learn to "travel" inconspicuously to the next place you need to be, rather than cutting the thread and re-starting.
I never bury threads unless I were hand quilting (rare). I just use my auto thread cutter and trim the threads.