Thanks to @Jakob for the help.
To get permanent customised CSS within the notebooks, I needed to create <myprofile>/static/custom/custom.css
in my .ipython
user folder folder.
This worked quite ok. I used the firefox's webdev tools to find the css items and classes in the ipython notebook and managed to get a monokai-ish style:

I also learned from here that you can inject javascript which might make it possible to add default content to new notebooks. I haven't tried this one yet though.
Edit: if interested, the css file lives here. The monokai colors are based on .cm-s-ipython
, which I think is similar what sublime text is using.