So, which one is the best method for deducting your home office expenses? The accepted best practice here is to use the accountable plan for the deductions because it doesn't create additional tax reporting needs the other methods need.
For instance, if you pay yourself rent from the S-Corp, then it creates a need to report that income as a Schedule E rental income, thus negating much of the tax savings. Same with the first option; that would require you to fill out a Schedule C on your 1040.
But under an accountable reimbursement plan, you get to record the expenses as such on the business, lowering your net income and repaying yourself for the expenses you pay personally for your home without also creating further tax liabilities from those payments, provided you don't also claim that amount on your personal tax return as deductible expenses.
There are qualifications that must be met to take the expense:
To calculate the expense reimbursement, take the square footage of your office space in your home and divide that by the total square footage of your home; this gives you the percentage to apply to each expense on an ongoing basis. Then you take that percentage and reimburse it to yourself as the employee of the company.
Questions?