How are you quilting? Hand, domestic sewing machine sit down or rack mounted? I have always had good results using the blue mark be gone markers by following the instructions and using a name brand one like Clover or Dritz. I always test first, never leave the marks on any longer than necessary and don't iron it or expose it to extremes in temperature. But in order to fully remove the ink the quilt needs to be completely submerged in water at some point.
But if you are the least bit wary about them some other options are to cut circles out of freezer paper and iron them on to the quilt surface and quilt around them and simply peel them off as go. This probably won't work with DSM sit down quilting because the way you have to scrunch up the quilt top to fit in your machine will most likely cause the freezer paper to come off before you get to it. Another option is to teach yourself how to DSM quilt using template rulers and quilt your random circles using the ruler template. You could experiment with a hera marker which is a plastic tool that doesn't actually mark the quilt it puts a crease in the surface you can follow.