What did the bush administration do to coordinate domestic security matters among a number of federal state and local agencies?

They established The United States Department of Homeland Security 

It was found as a response to the 9/11 attacks and deals with public security in all possible ways, from stopping terrorism, taking care of borders, customs, providing relief in case of disasters, management of law enforcement agencies, fighting cyber threats, and numerous other situations which might be harmful for the citizens of US.