There are two primary ways to keep your duplicates down.
1. If you are importing people from an existing database there will already be an ID assigned to them by that system. NationBuilder has fields for civicrm_id, ngp_id, state_file_id, dw_id, twitter_id, twitter_login, facebook_uid, and a few others. If we don't have yours included, then you can use external_id for whatever system you have. If you map one of those fields, NationBuilder will look it up to see if they are already in the system and then update their record.
NationBuilder also has its own "id" field which is automatically created whenever you import someone, but you only want to map that to your file if you are importing a list of people you previously exported from your NationBuilder account.
2. Most of the time though you will just be taking a list of email addresses, names, and/or phone numbers from some kind of contact list. Here NationBuilder will offer the profiles for deduplicating based on email address and then phone number.
If you have just a name for a person, AND you have some kind of state_file_id or external_id, then NationBuilder will import it because it assumes it's coming from another database.
All of that said, you will end up with duplicates in your database, and you can manually dedupe by following these instructions.