As @ccstone notes, asking multiple questions in on topic makes it hard to answer, and any follow questions rapidly become confusing.
If you mean adjusting the Notifications system preferences, that would probably have to be done mostly with UI control, which is definitely going to be tricky, and will change before and after Ventura since Ventura completely redid System Preferences/Settings.
This is relatively easy to do, just use an Activate a Specific Application action, Pause for the windows to appear, and then adjust the window position(s) with the Manipulate a Window action.
I don't know of any easy way to detect focus mode, or to trigger when it changes.
This is very easy, there is a Set System to Dark Mode action (or Light Mode, or Toggle).
As you can see this is already going to get confusing if we try to follow up each of these with additional questions, so instead, read through that, and then post a new topic with a specific question and we can work through that.