Each of the AUDMUX ports has its own set of registers that allows you to configure the port as desired. Please understand that you will be using six ports for three external signals. If AUD3, AUD4 and AUD5 are being used as external interfaces, then AUD1, AUD2 and AUD6 will serve as the internal ports to connect these signals to the SSI blocks. You are free to map the internal ports to the external ports as you want.
Since all ports are independent, they can serve as inputs or output in any combination.
For the details, I think you can read the i.MX6 Reference manual Chapter 60 Synchronous Serial Interface (SSI). Then try to change the register setting in the source code.
