Really depends on the context: "It seemed like you had been good together" - in the past, they looked good together "It seems like you have been good together" - in the present (right now), they look good together "It seemed like you have been good together" - I'm not sure when you would use this ... maybe if you noticed earlier but you still think it's true?

Ok, first. It's a little difficult when you don't have the context, but, I think it fits better like this: It seems like you have been good together. (if you still believe they look good).

Likes or as .. I Think It has seemed as you have been ......