Does it matter how it is allocated?
Absolutely, when reported in the Rental section.
It seems only total gain will impact the tax?
Of course. But when reporting in the Rental section of the program, allocation of sales price matters. If you show a gain on one asset and a loss on another, the depreciation recapture *will* *not* be correct, and in most cases the program just flat out can not handle that. Lets use two depreciable assets as an example, assuming both property improvements were done in the same tax year.
New roof, cost of $10,000 depreciated over 27.5 years reduces the cost basis by roughly $3,640 to $6,360 after 10 years.
Bath & Kitchen remodel, cost $10,000 depreciated over 27.5 years reduces the cost basis by roughly $3,640 to $6,360 after 10 years.
You sell the assets which you paid $20,000 for in total, for $25,000. That's a $12,280 gain of which $7,280 of that gain is recaptured depreciation.
You allocate $18,000 of your sales price to the roof. Subtract the $3,640 from the original $10,000 you paid and you get an adjusted cost basis of $6,360. So $18,000 minus $6,360 give you a gain of $11,640.
Now allocate the remaining $7,000 of your sales price the the kitchen/bath. Your original cost of the kitchen/bath upgrade was $10,000, minus the $3,640 from that gives the adjusted cost basis of $6,360. So your gain on that is $40. Where's the remaining $3,600 of depreciation you're required to recapture on this specific asset? It's just "gone". The math itself is correct, so the program doesn't see any "error" because mathematically, there is no error to catch. But legally, you've not recaptured all the depreciation as required by law.
While the program may not catch this in it's "final review" error checks, you can bet the IRS will.
