When you do machine piecing, use a different color thread in the bobbin than on the top spool holder. It will make ripping out seams easier.
To rip out a seam, cut every third or fourth bobbin stitch with your seam ripper. Then remove the top thread from the other side. It should come out easily, in one long strand.
To remove all the little bobbin threads from the other side, just use a piece of masking tape.