Box 3 on Form 940 should show ALL compensation paid to employees during the year regardless of other reporting (or taxable) limits. In the example in the original question, box 3 on the Form 940 would be $48,000. Then box 4 would be $18,000 and box 4c would be marked.
Box 3 total payments are defined by the IRS as:
Compensation, such as the following.
—Salaries, wages, commissions, fees, bonuses, vacation allowances, and amounts you paid to full-time, part-time, or temporary employees.
Fringe benefits, such as the following.
—Sick pay (including third-party sick pay if liability is transferred to the employer). For details on sick pay, see Pub. 15-A, Employer's Supplemental Tax Guide.
—The value of goods, lodging, food, clothing, and non-cash fringe benefits.
—Section 125 (cafeteria) plan benefits.
Retirement/Pension, such as the following.
—Employer contributions to a 401(k) plan, payments to an Archer MSA, payments under adoption assistance programs, and contributions to SIMPLE retirement accounts (including elective salary reduction contributions).
—Amounts deferred under a non-qualified deferred compensation plan.
Other payments, such as the following.
—Tips of $20 or more in a month that your employees reported to you.
—Payments made by a predecessor employer to the employees of a business you acquired.
—Payments to nonemployees who are treated as your employees by the state unemployment tax agency.
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