why use a chiller on a 46 gl tank.cooling fans over the top would cool the tank.u could get away without a pump.use a syphon method.syphon water from the tank through the chiller to the sump and make the return pump pump the water back to the tank.
been keeping reef tanks for 15 years had tanks from 10 to 180 gls.all had deep sand beds and all my tanks had zero nitrates.there could be other reasons your nitrates are high.are u filtering your make up water ro di.do u have wet dry with bio balls.try seeding the bed with some good live sand...