All federal agencies are funded through congressional annual appropriations. The funding for each agency is included in one of the thirteen bills that Congress considers each year. The EEOC receives its funding to do its work through the Commerce-Justice-Science appropriations bill.
After the President submits the federal budget to Congress, it then goes to House and Senate Budget Committees to formulate the annual budget resolution, which sets the budget totals for the entire federal government for the year. From there, the measure proceeds to the House and Senate Floors, where each chamber considers their respective resolutions and votes on them. The resolution then proceeds to conference to work out the differences between the two measures. The reconciled resolution is then presented to the House and Senate for a Floor vote.
After the budget resolution has been adopted, the House and Senate each establish the total funding levels for each of the thirteen appropriations bills. The following chart is a "road map" of the appropriations process starting at that
In addition to appropriations, Congress has an oversight role over federal agencies. Congress carries out this function by holding hearings and conducts oversight of agency enforcement operations, functions and policies.