Amilees Uncle,
When I was audited in 2011, the IRS auditor did not have any issue with my home office deduction through the 1065 business tax return, since he said it came out the same either way. Yes, I believe I have seen is correct for it to be listed in Schedule C & E, but since we are a husband & wife LLC required to file as a partnership, he allowed it. At the time the entry information was clearer, so I kept doing it that way.
