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Thanks for the question! Almost all of the Executive branch records that you seek are still under the control of the agency that created them (the National Archives and Records Administration does not have them yet). You will need to file Freedom of Information Act requests with the individual agencies. Depending on how many FOIA requests you want to make, it's going to require some great organization and a lot of patience; FOIA is an awesome tool, but slow. Our friends at the National Security Archive have an excellent introduction to the process on their website FOIA resources, history, and analysis.
For the records of the United States Department of State you will need to file a Freedom of Information Act (FOIA) request. The request needs to be made in writing. More information can be found here: Information Access Guide: U.S. Department of State - Freedom of Information Act .
For the Department of Defense their FOIA office contact information is here: FOIA . With defense you can also FOIA individual Combatant Commands, Military Services, or Defense Agencies. It can be pretty complicated.
The Defense Intelligence Agency is here: FOIA.
The Federal Bureau of Investigation (FBI) is here: https://www.fbi.gov/services/records-management/foipa.
The Department of Homeland Security is here: Freedom of Information Act (FOIA) | Homeland Security.
The Central Intelligence Agency (CIA) FOIA office is here: How to File a FOIA Request | CIA FOIA (foia.cia.gov).
Many of the executive branch agencies use FOIA Online which can be found online at FOIA - Freedom of Information Act and allows a person to make one request across multiple agencies.
As for Presidential Records from the period 2001-2014. The records of the George W. Bush (January 20, 2001-January 20, 2009) presidency are held by the National Archives and Records Administration at the George W. Bush Presidential Library and Museum. The records are made accessible through FOIA request and the Presidential Records Act (PRA). The FOIA page for the George W. Bush library is here: How to Submit a FOIA Request - The George W. Bush Presidential Library and Museum.
Presidential Records of the Barack H. Obama presidency (January 20, 2009-January 20, 2017) will take a bit of waiting. Under the terms of the PRA, presidential records are not available for use by the public (unless they have been previously placed in the public domain) and are not subject to the Freedom of Information Act (FOIA) until 5 years after the end of the Administration. Those materials restricted under the terms of the PRA will remain closed for 12 years after the President has left office. The short answer is that the records of the Barack Obama administration will not be available for FOIA until January 20, 2022. A recent update on the upcoming Obama library can be found online at Assembling the Obama Library.
Hope this gets you off to a good start and best of luck with your research.