| How does a Taxpayer apportion a CPA's fee?
Generally speaking, a CPA' s fees for the preparation of personal tax returns are deducted on Schedule A line 22, under Tax preparation fees. However, these fees are subject to the 2% Adjusted Gross Income Limitations.
Usually, most average taxpayers are unable to be obtain any deductions just on this item unless of course they have unreimbursed employee business expenses, casualty and theft losses.
So, it is prudent to determine what portion of the CPA tax preparation fees pertain to the LLC versus the Personal tax return. From what I can gather from your question is that the return was initially filed as a 1065 and 1040. Then an amended tax return was filed to report the activity presumably as a Single Member LLC and the entire business activity was reported on Schedule C.
If this is the scenario, then I would definitely deduct the fees for the preparation related to the original 1065 tax return along with a portion of the amended tax return that pertains to the filing of the Schedule C that reports the business income and expenses.
Your percentage breakdown of 50/50, in my opinion, appears reasonable considering that a Schedule C is relatively more expensive schedule to prepare along with the related Schedule SE. | 
