Your water tank would have to be very uniquely plumbed to drain into your waste holding tank...there should be no connection whatever between the fresh water and waste holding systems.
You should only be able to drain your waste holding tank via pumpout or through an overboard discharge pump. If you need to flush it out, pump out, then put enough water into it via the deck pumpout fitting--'cuz that sends the water into the tank at the bottom to stir up any sludge and hold it in suspension so it can be pumped out--to cover the bottom to a depth of about 6"...pump that out. Repeat...repeat...repeat...till you're pumping out clean water. Then, assuming that you have an overboard discharge pump, put another few gallons of water into the tank and turn on the pump to rinse it and the plumbing through it. You're done.
To winterize, add antifreeze through the toilet. If your toilet uses raw water (sea, lake, river water) disconnect the inlet hose from the thru-hull (prob'ly be a good idea to close the seacock first) and stick it into a gallon jug of antifreeze. Flush the toilet to pull the whole gallon through the entire system and into the tank.
If you need to drain the water tank, you can either just disconnect the pump from the line coming out of the tank and let the tank drain into the bilge, or you can turn on every faucet on the boat and drain it overboard through the sinks...assuming that they do drain overboard and not into a gray water tank. If you do have a gray water tank, pump it out and rinse it out the same way you drain and rinse the black water tank.
When winterizing the fresh water system, drain and bypass the water heater. Water heaters have drain petcock at the bottom...bypass kits are available from most marine retailers. Do NOT put antifreeze in the water heater...it'll take forever to flush it all out in the spring! If you want to avoid using antifreeze in the fresh water system altogether, blow all the water out the plumbing using an air compressor...which can be made a lot easier by installing some quick connect couplers in the fresh water lines where needed.