So keep the static navigation transparent, go to Appearance > Elements and edit Home Page Transparent Header. Select transparent for the navigation background colors:
https://docs.generatepress.com/article/header-element-overview/#navigation-colors
Then the colors you set in the customizer (Colors > Primary navigation) would work for the sticky navigation color.
As for the header question, I’ve answered it here below Please keep the conversation separate in each topic:
https://generatepress.com/forums/topic/question-header/#post-1403523
Please keep in mind that we cannot do things in this support forum – we are happy to provide instructions on how to get it done but you will need to follow the steps.