Okay stupid question I know... It's my first year running water in my rad, The question is do I need to flush the cooling system and top it up with antifreeze or can I just drain the water and let it sit empty over the winter? I'll be storing it in a non heated space.
Did you run any additive in the water? I ask because next summer when you want to run plain water, put a couple capfuls of Water Wetter in there. Water is corrosive, Water Wetter adds some anti-corrosion.
As for the winter, yes, put coolant in it after dumping the water out.
Which is why you should be running distilled water not the stuff out of your tap or hose.
Distilled water is still corrosive. Which is why I have Water Wetter in mine, regardless of the fact that I used only distilled water in the bike. Not frickin' tap water.
You can leave the system dry over winter. Minor pockets of water sitting in low spots in the system won't cause a problem - the water has room to expand if it freezes. Some cooling systems have more than one drain location, in order to allow bigger low spots to be emptied.
Put a piece of tape with "NO COOLANT" written on it over the ignition key hole, to avoid forgetful mistakes next spring.