There are two places a contact may exist: in a data extension linked to an attribute group that is marked "Use as Root", or on the All Subscribers list. The "ROOT" data extension is essentially your MASTER data extension.
As you mentioned, you can only use as root when you have a 1 to 1 relationship setup. This is done to uniquely associate the contacts in your data extension back to your Contacts so you're able to send successfully to them in a JB Interaction. Your 1 to 1 relationship should be something similar to "Contact Key" = "Subscriber Key" (or Email Address) for this to work properly.