Overall he says:

The procedures ensure that an individual will be transferred from civilian to military custody only after a thorough evaluation of all of the relevant facts, based on the considered judgment of the President’s senior national security team, and not a rigid statutory requirement that does not account for the unique facts and circumstances of each case. This decision requires the concurrence of the Attorney General, Secretary of State, Secretary of Defense, Secretary of Homeland Security, Chairman of the Joint Chiefs of Staff, and Director of National Intelligence.

Also,

The procedures clarify that, until an individual is formally designated a covered person, federal law enforcement agencies should follow their standard practices. The procedures also make clear that, even after an individual is determined to be a covered person, a transfer to military custody may only occur once it is clear that it will not disrupt ongoing law enforcement and intelligence operations. In the event an individual is transferred to military custody, the procedures provide that the Federal Bureau of Investigation will retain its lead responsibility for coordinating the investigation and interrogation of the individual until a disposition decision is made.

Obama says:

In essence, these procedures are intended to ensure that the executive branch can continue to utilize all elements of national power -- including military, intelligence, law enforcement, diplomatic, and economic tools – to effectively confront the threat posed by al-Qa’ida and its associated forces within the framework of our legal authorities, and will retain the flexibility to determine how best to apply those tools to the unique facts and circumstances we face in confronting this diverse and evolving threat.

Obama also laid out circumstances in which military custody will automatically be waived:

• When placing a foreign country’s nationals or residents in military custody will impede counterterrorism cooperation;
• When a foreign government indicates that it will not extradite or transfer suspects to the United States if the suspects may be placed in military custody;
• When an individual is a U.S. lawful permanent resident who is arrested in this country or arrested by a federal agency on the basis of conduct taking place in this country;
• When an individual has been arrested by a federal agency in the United States on charges other than terrorism offenses (unless such individual is subsequently charged with one or more terrorism offenses and held in federal custody in connection with those offenses);
• When an individual has been arrested by state or local law enforcement, pursuant to state or local authority, and is transferred to federal custody;
• When transferring an individual to military custody could interfere with efforts to secure an individual’s cooperation or confession; or
• When transferring an individual to military custody could interfere with efforts to conduct joint trials with co-defendants who are ineligible for military custody or as to whom a determination has already been made to proceed with a prosecution in a federal or state court.

Also,

When a national security waiver is issued or applies, standard operating procedures would continue to be followed, and the terrorist suspect would remain in law enforcement custody.

The President’s procedures also make clear that the Attorney General, in consultation with other senior national security officials, has the authority to issue additional waivers for categories of conduct, or for categories of individuals, or on an individual case-by-case basis, when doing so is in the interest of national security.