The best way to add subscription add-ons for an account is to create them as separate line items on an invoice through the Account API.
Natero currently includes subscription add-ons (or discounts) as recurring revenue and line-items when it pulls data from 3rd party systems such as Chargify or Recurly. For example, a 12-month subscription with an amount of $1000 and $200 add-on will generate an MRR of $100 for the account having that subscription.
Details of the add-on (or discounts) can be added custom subscription dimensions for the corresponding subscription in Natero.