The tax preparation fees in general are subject to the 2% Adjusted Gross Income (AGI) limitation and includable on Schedule A.
This means that the tax preparation fees are deductible only after they exceed this 2% AGI amount. Thus, in general for most taxpayers these fees are really not tax deductible after accounting for the 2% AGI limitation.
However, in your case, you incurred $1,000 in tax preparation fees and you have a sole proprietorship business. So, you should consult your CPA and ascertain what amount of the fees are attributable to your Schedule C.
I would recommend that you perhaps claim a minimum of 50% of fees on Schedule C and balance you can claim on Schedule A. There really is no way to avoid part of the fees being subjected to to the 2% limitations. But, it is safe to claim 50% on your Schedule C, provided you don't have a complicated tax return with inclusion of several schedules such as schedule A, B, D and passive lossess etc apart from Schedule C.