Look under Business Info >> Shareholder information and edit the Shareholder that is a trust. Be sure you checked the box for "This shareholder is not a person..." and selected "Trust" from the drop-down. This choice should allow you to enter an EIN instead of a SSN for the Trust.
You'll also notice that Form 1120S page 2 Schedule B question #3 is marked "Yes." This requires additional info on Schedule B-1. Enter the name and tax id number of responsible party for the Trust (typically the Trustee).
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