One of the checks and balances is outlined in Article 2, Section 2 which states that the president shall appoint the officers of the United States with the advice and consent of the Senate. That almost never means advice, only consent, which is usually but not always offered.
Here are few links with background on the process--at least the committee hearings--the current nominations are going through:
For Secretary of State: Hillary Clinton. Hearings in the Senate Foreign Affairs Committee.
For Attorney General: Eric Holder. Hearings in the Senate Judiciary Committee.
For Transportation Secretary: Ray LaHood. Hearings in the Senate Commerce, Science and Transportation Committee.
