What boat Chris? Where is your heater?
Heater installs can vary a bit. The bottom line is you need to drain it. Find the core. Pull the hoses. Blow it out with some low PSI air.
I installed a pair of Prestone Flush Kit Ts in the heater lines on my boat. Their down in the bilge, I pull the caps, gravity drains the water into the bilge. Done. You can also use garden hose quick release fittings, similar to how your exhaust manifold hoses are on most newer boats.