Under default Monokai, I cannot replicate:

However, if I change the Default Style > Background for Monokai (to a green similar to your second screenshot), I can see it:

It’s because Monokai (and most themes) hardcodes every background color for every style, rather than using “inherit”. Here’s an example using the default style:

The theme color choices aren’t always perfect, and not everyone is going to agree with color choices made. As such, you can customize to what you want.

If you want most of the backgrounds for your theme to inherit from the “default background” rather than being hardcoded, you can go through and right click the background color for any that are the default. (Or, as a footnote, I will also explain a process that you can edit the XML for your customized Monokai, to automatically change anything that has a background that matches the monokai default background to inherit from default background, so that you can do it in a lot less time.)

What I need is a better highlighed line I am working in, its black on dark that has nothing to do with highlight.
…
If I try to change it via Style congiruator the line will be solid in the color I choode doesnt matter for fore or background.

Which “highlight” do you mean? And I am not sure what you aren’t liking about it when you change it.

• Current line highlight:
  • default Monokai:
  • set it to something else:
  • it does exactly what I expect: it changes the current line background color 0x3E3D32 to something based on the color I selected.
• Selected text colour:
  • default:
  • modified:
  • again, it does what I expect
• Smart Highlighting:
  • default:
  • changed to cyan:
  • this one, it’s actually combing the selected color with the normal background color, so it’s not exactly the same color you chose; but again, that’s not unique to Monokai
• Find Mark Style: used when you use Find > Mark dialog
  • 
• Mark Style #: used when you use Search > Style … Token options:
  • 

There are a few other, less likely, choices that you might mean by highlight. But rather than showing that I think it does what’s expected, it would be better if you were more specific about what you were doing, and what you don’t like, and what you would like.

Footnote: Make Monokai backgrounds inherit quickly

I assume you have a copy of Monokai.xml in %AppData%\Notepad++\themes\ .

1. Exit all copies of Notepad++
2. Copy Monokai.xml to Monokai_custom.xml
3. Edit Monokai_custom.xml with Notepad++
4. Confirm that <WidgetStyle name="Default Style" has bgColor="272822" – if not, manually edit it to use that
5. Search > Replace, set Search Mode = Regular Expression
   1. FIND = (?-s)bgColor="272822".*\KcolorStyle="(?:(2)|(3))"
      REPLACE = colorStyle="(?{1}0)(?{2}1)"
      REPLACE ALL
   2. FIND = (?-s)(bgColor="272822"(?:(?!colorStyle).))*\h*/>
      REPLACE = colorStyle="${1} colorStyle="1" />
      REPLACE ALL
   3. On the “Default Style” line again, delete colorStyle="1"
   4. Save the file
6. Exit Notepad++ and re-launch it
7. Settings > Style Configurator > Select Theme = Monokai_custom

Now if you change Monokai_custom’s default background color, it should propagate to all the other styles (both normal text and each language), so it really changes the background throughout.