You need to clarify what you have, is it a "water heater " with a tank that holds gallons of stored water, or is it a tankless "heater of water" which is attached to your boiler on the inside which heats the water which goes into a separate storage tank as you use it.
If you are going to bypass the coil in the boiler you just need to install a shutoff after the coil so water does not fill the tank.
You also should drain the tank more often when you do not use it. Plenty of maintenance issues are about to start, get ready for lots of sediment.
My opinion is to just get rid of the tank, and use the tankless year round. That way you do not have maintenance issues with both systems. The tankless will also save you money year round because it heats the water more efficiently than your boiler ever could. Even though it is on in the winter, you are still heating and storing water for "when" it may be used.
Get rid of the tank.