The amount of freeboard necessary between the primary and emergency spillway depends on many variables and will vary from pond to pond, but unless you just experienced an unusual rainfall event, it does sound like you need more.
Be careful adding height to the spillway because no matter how you compact it, fill material will always erode easier than natural undisturbed soil. On page 31 of USDA Agricultural Handbook 590, it talks about this saying that an auxilliary spillway should be excavated into the earth for it's full depth, otherwise vegetation or riprap should be added for protection.
http://www.in.nrcs.usda.gov/pdf%20files/PONDS.PDF
