how to modify SOPC generated uart?

I might have misunderstood your question, so correct me if I'm wrong.

You want to use the SOPC system to send data via UART to a VHDL logic block, which would process the data and send it back over the UART to the SOPC system?

UART is not the best way to do this, but if you are using it to prototype something that has to communicate with a separate UART device, your method will work. You just have to implement the UART protocol in your VHDL, or instantiate an existing one and interface to it via an Avalon/Wishbone interface.