You basically just need to complete the extension form and check a box that it will be e-filed. But while we are on the subject, why would you need to extend a 990N?
from the instructions at IRS:
If your 990-N is late, the IRS will send a reminder notice to the last address we received.
While there is no penalty assessment for filing Form 990-N late, organizations that fail to file required Forms 990, 990-EZ or 990-N for three consecutive years will automatically lose their tax-exempt status. Revocation of the organization’s tax-exempt status will happen on the filing due date of the third consecutively-missed year.