Sorry, I got a bit confused there... Could you please explain your question some more in a different way?
Let me see if I can clear up how those parts work in relation to custom profile fields:
You create the custom fields from s2's General Options.
This will show the fields in the registration forms, and in the user profiles, and these two places would allow you to enter values into those fields for the user.
The users list, or the emails, can use the custom field values, but they don't control the field's values. So whethere you use the custom field in the email or not, doesn't affect the field itself at all.
If you create a custom field, it will now be available in the profile of users that existed from before the field was created, but they won't have a value, even if it's a required field, because no value was entered yet, since the field didn't exist when the user was created.
Does the above help clarify things a bit?