Hello @ Cassius
Thank you for bringing your question to the Quicken Community today!
When you add your mortgage bills to the Bill Manager feature in Quicken and pay them via Quick Pay or Check Pay, yes, the payment will be made through that system. We have quite a few resources available including How to move from Quicken Bill Pay to Quicken Bill Manager, which will guide you through the set-up process, as well as Quicken Bill Manager: How To Make Payments Using Quick Pay and Check Pay, which has helpful information about making the payments.
Please let us know if you have any further questions.
Thank you
- Quicken Diana