Dynmically calling VF config

System

We have an infrastructure set up in TeamSite so that the DCT is dynamically put together when called. This allows for resuse of fields when possible and short DCT configurations.

Let's say you have 2 sites, each in its own branch. Each branch has its own css which is exactly the same except for the color palette (e.g. in Site_A the header is blue and in Site_B the header is red). Is there a way to use the same textarea item for both branches and configure the VF tool to accommodate the different color palettes with 2 different css?

In other words, could the VF_config.xml for the textarea of the DCT be determined depending on the branch? Or would you have to create two separate templates where each template was pointing to its own VF_config.xml ?

What we're hoping to avoid is having to recreate essentially the same template just to call a different VF_config.xml for a different color heading.

The version of TeamSite is 6.1

Thanks.