Water Heater Radiator Flooded - Help!

We were trying to flush the pipes by turning on the water valve to the system and draining it out of drain valve at the bottom. Well the drain got closed and the water wasn't turned off. I came down downstairs to realize this as it was spilling out what I imagine is the relief valve which is just a pipe out of teh top of the boiler. I believe it's a 1 pipe system. Now it's turned off and isn't heating at all on a very cold day in NY. I'm not sure how to fix the water level, do I just take water out until the water sight gauge shows the level midway in the glass? Any advice would be greatly appreciated. Thank you.