Geoff,
The box you refer to helps you avoid picking more than one player at any position. For example, say you want a specific CF but you're not sure someone else won't take him. You can load CF's into a 'group' in the order of preference, and then tick that box for all of the options after the first one. Then if and when you get one, the rest will be deleted from the proxy list, and the system will move on to your next 'group'.
And yes, we roll with unique ballparks, and you are free to take one anytime during the draft.