I don't prewash fabrics, but someone elsewhere on the forum posted a tip several days ago. She basically flat folds her yardage and pins the folds together at both the selvedge end and the fold end before putting them into the washing machine. I imagine this would work for jelly rolls and fat quarters too to prevent tangling. It seems to me you would need fairly large and sharp safety pins to do this.
You could also probably just machine tack the pieces together (move from one tack to the next and afterwards cut the threads connecting the tacks). Or maybe just use an ultra-long basting stitch on the machine; I know mine has one that is about 2 inches long. It would be really easy to pull the basting stitches out afterwards.