You can link an account by tapping Menu then Account Management on the title screen or Misc., then Account Management, then Create/Link a Nintendo Account.
Note: If you do not have a Nintendo Account, please see What is a Nintendo Account?
■ Steps
1. Open the Account Management menu from the Menu on the title screen or by tapping Account Management in the Misc. menu on the home screen.
2. Tap Create/Link a Nintendo Account.
3. Input your email address and password to log in. If you have already signed in to your Nintendo Account, tap "Select this account".
Note: Double check the Nintendo Account being displayed carefully before performing this step.
For instructions on how to transfer your save data, see How do I transfer my save data? (When changing to a new device, etc.)