For an S Corporation (Form 1120S) return in Intuit ProConnect Tax Online, the option for marking the return as the final return (i.e. Box H(1) of Form 1120S) is hardly easy-to-find in the Input Return module:

To toggle for this box to be selected in ProConnect Tax Online, go to the following menu in the Input Return module:
General >> Miscellaneous Information (Misc. / Other Info.) >> Miscellaneous Information

In the “Miscellaneous Information” page, halfway down, there is a checkbox for marking the return as final:

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