When you're sewing any star block, it really, really helps to sew two sections together, press the seam open, and then trim the points off. If you do this, you don't have the really thick joint to sew over/under/around. On a six-piece star, you need to sew two pieces together, press the seam open, then sew the third piece on and press open that seam -- then trim the points. You will end up with a really nice hexagon without the lumpy center.
It's a lot more work, but your long-arm quilter will appreciate it and, if you handquilt, it will make your job easier.