Ok I got it... It was just a silly bug or something. (I will not blaim STSDEV for this though!)
So I define my Content Type using the definition xml file as usually. Add a FieldRef and link that to the Field element and in the Type attribute I but the name of my custom field type.
[FieldRef ID="{GUID}" Name="MyField" /]
...
[Field Type="MyCustomField" ... /]
The bug was that I used DebugDeploy or DebugReDeploy but somehow I needed to go in and manually deactivate the Feature and then re-activate it. Don't know if this is a bug or just some strange things in my setup.
Thanks,
Sigurbjorn