Just to make sure, do you mean you want the header (with logo block etc) having a different background color when viewing a private conversation?
I would think the easiest way to do that is to add
Code:
#header {
background-color: red !important;
}
in conversation.css
This is with the disclaimer that I understand the XF template system correctly and that css will only be called when viewing a conversation. If you want to do it with extra.css you will most likely have to use conditionals.
Another way would be to use conditionals in the header html to apply a class if you are looking at a conversation. I would say one single CSS edit to conversation.css is easier.
But if editing templates is a concern, have you considered the Template Modification System add-on?
It doesn't change any of the original templates and is basically a find and replace type system.
If a new version of XenForo is released all of your templates remain "up to date" and it would be a lot less work to get template modifications to work with the new version.
EDIT: And again MagnusB is right, but that's still a template edit.
All I know is the XenForo version works perfectly. It's very highly thought of here and I think quite a few people here are advocates for it being included as a core feature.