Cryn, thats exactly what I would do, if you have a locking stitch, use it, dont cut your threads go down the whole row, the divide the thread between the two ends and bury them into the quilt, you may waste alot of thread but you will save so much time :-D
Your quilt is beautiful, and you will enhance the 3D effect with in the ditch quilting, meandering will take away from that IMHO :-D