Yes, but if you have the original land value entered, ProSeries pretty much makes you do it unless you specifically tell it not to.

As for the allocation, I'll use the Property Tax statements and use that ratio.  I know a lot of people claim those amounts are way off, but in my area, they seem to be reasonably close.  At least in my area, the property tax valuations are done by certified appraisers (who work for the city/county), so they should be accurate.  The only difference is that sometimes they don't have access to the interior of the building, so they need to make some educated guesses.

But as I mentioned before, the only time I can think of when it matters is if the building decreases in value (combining them will alter the 1250 gain vs 1231 gain).  There could be other things too, but that is the only scenario that comes to my mind.