Any ad ran, either manually or through the Ad Manager should count towards the creators 3 minutes per hour of required ad time in order to earn the 55% split. After reading the following text in the Ad Manager support page, it became clear that manually running ads while I am taking a quick break to stretch or grab a drink, those ads are actually hurting my overall revenue split.

Can Affiliates earn 55% ad revenue splits by running ads manually, or via a third party tool?
No. Only ads run via Ads Manager (at 3 minutes or more per hour) qualify for the 55% ad revenue split.

Make ALL ad’s count towards creators revenue split, regardless of how they are ran.