Adjust colours and keep them after a update?

I think, an update will upload the normal css files, so it will overwrite your changings.
I think only the special settings for standard responsive layout (on the bottom of layout) will not be overwritten.
@hekla: is this true?
[Personally I would use background-color: #eee) -->less agressive

Yes, there is a solution: you activate the custom jem.css and write your changed file there in!