Is this how Scatterer + EVE should look like ?

[S3M1CZ]

So I've just downloaded my first Graphic mods - EVE + Scatterer. They work but.. look a bit glitchy.

http://imgur.com/a/u9D1E

Is it just me and it looks absolutely normal or..?

[DrLicor]

Totally normal  

But I think what you mean, try to disable the Godrays in the startup menu from scatterer. Godrays are responsiable for those bright dark section because the sun is quite low and shines on those mountains there.  
That orange section is from the last generation of scatterer and it totally fine. And indeed, cities can look a but ugly upclose, especially with small planets like Kerbin. 

If you don't want the cities anymore, you can delete the folder in the BuilderCo folder of EVE.