Client retainers land in your business account, but that money is not a paycheck yet. How it becomes personal income, and what paperwork that requires, depends entirely on how your fractional practice is structured.
Owner's draws from a sole proprietorship or LLC
If you operate as a sole proprietor or a single-member LLC taxed as one, paying yourself is mechanically trivial: transfer money from the business account to your personal account. That transfer is called an owner's draw. It is not a salary, no payroll runs, and critically, the draw itself is not what gets taxed. You owe income tax and 15.3% self-employment tax on the business's net profit for the year, whether you drew out all of it, some of it, or none of it. A fractional CFO who nets $200,000 and only transfers $120,000 to personal accounts is still taxed on the full $200,000.
The practical discipline is to treat draws as a routine: a consistent monthly transfer sized so that what stays behind covers your quarterly estimated taxes and business expenses. Executives who drain the account after every retainer payment are the ones scrambling at each 1040-ES deadline.
A reasonable salary once you elect S corp status
An S corp election changes the mechanics completely. You become an employee of your own company, and the IRS requires that you pay yourself reasonable compensation through actual payroll before taking profit out any other way. That means a recurring paycheck with income tax withholding and payroll taxes, quarterly payroll filings, and a Form W-2 issued to yourself each January. Profit beyond your salary comes out as shareholder distributions, which avoid payroll and self-employment tax, which is the entire point of the election.
Reasonable is the operative word. The salary should reflect what companies pay for the executive work you actually perform at the hours you perform it, and your own retainer agreements are strong evidence of that market rate. A token salary with large distributions is the classic S corp audit flag.
Keeping client money and personal money separated
Whichever structure you use, run the practice through a dedicated business bank account. Deposit every retainer, board fee, and project payment there, pay business expenses from it, and move money to personal accounts only through your chosen mechanism, draws or payroll plus distributions. Commingling is not just an accounting annoyance: for an LLC it can undermine the liability protection you formed the entity for, and for everyone it makes Schedule C or the 1120-S a reconstruction project at year end.
A workable rhythm for a multi-retainer practice: retainers in, a fixed percentage swept to a tax sub-account immediately, a consistent monthly draw or paycheck out, and a quarterly review where you true up against actual profit. Your pay becomes predictable even when engagement mix is not.