You need to delete the 960×90 header image and then separately … in another part of the dashboard, install your logo.
When you are at appearance > header the only thing you can do there is select “remove header image”. You cannot upload your logo here UNLESS it is 960×90 or you have built another image which is 960×90.
In nearly all cases you will need to install your logo image separately in a header widget area.
Here is some advice about installing adsense text in the graphene header you can see here what you need to do to set up the header widget:
http://wordpress.org/support/topic/ad-sense-widget-in-header
You can also search and find some info about activating the straight ‘header’ widget area.
You can search and find how to write the HTML code to display your logo and put that in the text widget which you can place in the header.
You can also consider installing an image widget which I have just learned about here:
https://forum.graphene-theme.com/graphene-support/image-widget-where-is-it
I am just learning this myself and working my way down from the top I have found this header area a bit complicated for a simple edit.
