On a 1065 we can do special allocations by $ or by %. On a 1120S there is no such thing as a special allocation.  So the way I've done it in the past on actual split-year is to override the Schedule K-1 and make sure I have a supporting workpaper in my files for it.

If you were to allocate based on # of days versus an actual year-split you would go into the Weighted Average Ownership Percentage Worksheet. Then the software will do the math for you.