What you use often depends on the question. Let's say I want to meet someone in the cafeteria and I want to know when he will be there. An answer could be "he doesn't often eat breakfast but he always has lunch".

ya I think both are possible

Both are correct but the meaning is very slightly different : "He doesn't eat breakfast often" just means he doesn't eat in morning often and "He often doesn't eat breakfast" means the same but will be used in a context where you talk about his eating habits (for example a Doctor would use the second form to criticise the person's eating habits) I don't know if it is clear >.< ... In short use the first one :)