The congress is made up of the upper (senate) and lower (house). and each has its roll in government as well as the executive branch. Vito power I think rests with all three depending on ?? I think a EO can be vetoed but I am not sure of the qty needed, and if both houses are needed for an override.
The Federal government is set up in three branches: Legislative (Congress, made up of two houses), Executive (President and departments and agencies), and Judicial (Courts, from Supreme Court down). Creating laws normally require cooperation of the Executive and Legislative branches working together. Congress (both houses) must pass a bill and then the President signs it to become law. The exception to this is if Congress passes a bill and the President vetoes the bill, it can still become law by each house of Congress voting to over-ride the veto by a minimum 2/3 vote.
Back to the cooperation aspect: for a law to be effective, it must be enforced by the Executive Branch. Criminal laws are enforced by the Executive Branch through various law enforcement agencies (FBI, DHS, ATF, etc.), prosecuted by the Dept of Justice, and adjudicated in the courts (Judicial Branch). Laws with administrative instead of criminal purpose are implemented by the departments and agencies through regulations, such as the Department of Interior regulations on firearms on public lands.
The purpose of the Executive Order is for the President to give directions to departments and agencies on how to implement laws. Usually this happens by the EO telling a department what to include in their published regulations. Congress can override a published regulation through a special vote, but only for a limited time after the regulation has been published. Past that, it takes either a new law (which of course follows the above process) to invalidate the regulation. Alternately, a civil suit in the courts may argue that the regulation is invalid because it is did not comply with the law it claimed to implement. That is how EOs and regulations can be stopped through the Judicial Branch, in the same manner as the courts may invalidate a law by ruling it unconstitutional.
All the above is how it is supposed to work. The topic of judicial overreach (creating laws from the bench) deserves its own discussion.