Pro Tools is capable of "Total Recall" of all session parameters, including Soft SampleCell Banks and Instruments. For this to work properly, it is imperative that the Sessions and Banks are Saved and Closed in a specific order:
When you are ready to shut down a session, first go to Soft SampleCell and select File > Save All Changed (if prompted, direct it to the Hard Drive and folder where you want the Bank or Instrument saved).
Next, switch to Pro Tools and select File > Save Session.
Close the Pro Tools session.
Close the Soft SampleCell Bank.
Finally, close the Pro Tools session.
Reopening the session should now automatically launch Soft SampleCell (if necessary) and open the correct Soft SampleCell Banks and Instruments.