One thing that I have found useful is to spend time wire framing the web application at the beginning of the project. And then go through the sketches with both themes. That should help giving everybody a clear view of the target. My experience is that the more time you spend in this phase working out the details and figuring out the overall workflow, the less time is wasted at a later stage.
Then, after the initial planning, I think it makes sense to let the themes work separately for a while: The design people creates the basic design and turns it into html and css, while the Yii team defines the database structure and use Gii to auto create models and CRUD.
You could then start merging design and functionality by having the themes working together to get the overall design integrated into Yii. My experience is that several iterations is required for this.
I agree with what Trond said. I myself am developing a web app using Yii. In my case, the designer does not understand html / css, so he only made the psd. Then I hired a front-end developer to create the html / css ( only basic .html file) from that psd. My part is to develop the back-end ( database structure, app logic, etc.) , so we had the process running together, while I’m developing the back-end, the front-end developer is developing the html / css.
But there are some things to be considered. If, like my case, the process of developing the front-end and back-end is done at the same time, make sure that you create the wireframe first, so that the team got the picture of what the app will look like, especially the placement of the elements, so that the process of merging design and functionality will not consume much effort and time.