Checked means it is on or active.
I don't move my ship from team 1 spot. If I want more players on my team I choose Some other ship I like. I then add ships to my opponent or team 2's side. It would seem like the problem is when you move and then replace your ship. Are you choosing your enemies or letting the computer choose for you. I always do mine manually. Never checking undistributed ships. Hope this helps.