the probably check it to see if the domain belongs to someone that has been banned from YPN in the past.
I know google does that, but I am not sure with YPN though they may check if the applied domain is banned from beta.
ahh thats the gist of my question. I have most of my domain in private. So if they check, how would they know it's me?
It it is set to private then they will use other methods to see if the user who applied has been banned (cookies?, IP?). You shouldn't have to worry about it unless you did something wrong.