Yes, both cards can be utilized for Folding@home. Each GPU card will be given a separate Work Unit to process. In the older v6 client, adding the “-gpu N” flag (N starts at 0) would tell the client which GPU to use for folding. In the newer V7 client, the installer should automatically detect a multi-GPU setup and will configure itself to use them. Sometimes it has difficulties with mixed brands of GPUs. When this happens, our Guide pages may be helpful.
To adjust the configuration, change V7 to advanced mode using the drop-down menu in the upper right-hand corner, then under Configure -> Slots, edit the GPU slot and adjust the indicies. If you need help, consider posting in our Folding Support Forum.