[pm mastering studio]

you can use it but than you should select the I/O in your hardware which means you loose all the advantages of your ProTools TDM system. (low latency, enabling realtime effects, etc...)

One way to do this is to enable the Thunderbolt card, record all your tracks, return to the TDM hardware setup (lossing the outputs/inputs on the thunderbolt card) and start mixing.