I use prosystem and this is what I do. Lets say you have a stepped up basis in rental property when one spouse died. Since CA is a CP state, you have 100% step-up.
Force regular depreciation to be taken up to the DOD on the old assets on the depreciation schedule. These will be gone in next years proforma.
Input new (separate) land and building etc for the asset portion stepped up with a date acquired as DOD of the spouse. (and I list Building-Basis step up $xxx,xxx)