Clarify how new employees or contractors will get paid using this free compensation agreement template. Nonprofits report bonuses (including signing bonuses), and any compensation based on incentives, on Form 990, Schedule J, Part II, Column B 2 (ii).This article on exit agreements for nonprofit executives discusses when such agreements are appropriate and what should be considered. A discussion of best payroll practices for 501(c)(3) and other nonprofit organizations. Employment tax treatment of officers of taxexempt organizations, including those who are not compensated for their services. Part seven of our 990 series dives into publicly disclosing officers, directors, key employees and other highly compensated employees. The IRS guidelines and nonprofit travel and expense policy tips below are designed to help you shape a more effective policy in your own organization.