You don't have to remove the basting stitches, do you. If they are in the seam allowance I would leave them. The whip stitching is right on the edge of your piecing. The basting stitches end up on the back side of the fabric and the whips are on the top. I am assuming you are doing applique.
For better answer, a picture or link to your work or pattern would be very helpful.
hope you get the info you need.
peace