I want to use my custom masterpage as a site masterpage and keep the default "seattle" masterpage in the settings view ("System master page option").
Is this possible?
You have 3 options:
If you open a page in SharePoint Designer you can see a MasterPageFile setting which can be modified:
Additionally you can also set this through the UI, by navigating to the Site Collection Settings --> Look and Feel --> Master Page. Here you can choose the Site and System Master page separately.
Also, this can be done through Powershell,
I have posted that earlier here Apply master page to the settings page
Yes. You need to open the Site Settings -> Master Page and select
Site Master Page = Your custom master page
System Master Page = seattle