Pradeep, can you describe the two entities separately, i.e.
You have only one site that you want to submit.
You are asking about submitting to numerous directories that all look alike but have different domain names.
If the above is what you are saying, then there is insufficient information, but they sound like they are worthless directories.
Or are you saying that you have a collection of directories and you are submitting each one to all the rest?