I'm with the stormcloaks and now have a truce with the imperials and we gave them Riften, but what actually happens after the civil war? Do you take Riften back or?....

In order to complete the CW questline you have to gain or regain control of all nine holds. Any holds ceded to the opposition during the ceasefire will be taken back in a military action of some kind. So the answer to your question is: yes, you will be taking Riften back.