Receiving deductions from your business account is easy - as long as they meet the definition of a business expense (ordinary and necessary for the business), you will take them as a deduction when you file your business tax return.
As an S-Corporation, you are required to pay yourself reasonable compensation in the form of a salary. You should use a payroll provider to ensure compliance with all federal, state and local income tax withholding and submission requirements, as well as to handle or facilitate workers compensation and federal and state unemployment taxes. While it is possible to do this yourself, it can be very tricky and there are penalties for doing it incorrectly. Intuit offers payroll services through Quickbooks, our accounting software, so it might be worth it to check it out.
In terms of the expenses that you paid with your personal funds, I would create an expense reimbursement form that you use to reimburse yourself for those costs - similar to what you would use as an employee, submitting expenses to an employer. While this may seem like you are moving something from one hand to the other (you own the company that is paying you), the IRS sees you and the S-Corporation as two separate entities. This process of creating a formal reimbursement form that you report expenses is also what you should use for things like business mileage, business meals, travel, cell phone costs, home internet and home office expenses (best practice: create a home office spreadsheet that mirrors the IRS form, and create a reimbursement form by mid-December to reimburse yourself for home office costs). This is the cleanest and best way to incorporate all of your business income and expenses into your business account and remove the "personal account" aspect of your current situation.
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