Setting the pipe invert near, or below the pond bottom in a sump, will help to dissipate energy and minimize side slope erosion during high flows. In a wet pond I would set it with 6-12" water above the crown. In a dry pond you could use a sump, or set it within a foot of the bottom with appropriate scour apron at the outfall. As noted by CVG, you should the design for the tailwater, eg. check the max design flow with the max WSEL (a culvert nomograph - flowing full - is a simple way to check the last pipe segment HGL). I also recommend limiting the inflow pipe to 2% max slope, using a drop at the upstream CB as needed, so that inflow velocities are between about 3-10 fps for the max design flow.