Once in command, Montgomery laid down the rules to be followed in August 1942

When General Montgomery appeared on the scene, he "stole" two days of command from General Auchinleck. Montgomery did not believe in "Jock columns or battle groups". At least on paper, he wanted to fight divisions as intact units and in a somewhat contradictory fashion, said he would fight brigades as brigades. In the desert, they were used to having brigades as the normal fighting unit. In the past, they had often treated battalions as if they were brigades, but Montgomery was opposed to doing such. He wanted the divisions to hold their ground with no plans to withdraw any further. Montgomery tried an Australian hat but he did not understand how they were worn. Montgomery eventually settled on wearing a beret as his signature headgear. It turns out that Montgomery had an Australian connection, because his father had been Bishop of Tasmania at some point.

He disliked some of what Auchinleck and Eric Dorman-Smith had thought was a good idea. There were not more mentions of "boxes". He also did not like the term "consolidate", which he thought should be referred to as reorganization. Montgomery also wanted to use a real Chief of Staff, unlike Auchinleck's system of using an assistant chief of staff in Eric Dorman-Smith. He also expected when he issued orders that they would be acted upon, they were not to be a topic for debate.

There had been an idea that men should not wear their division insignia ("flashes"). Montgomery disagreed and said that flashes should be worn. Another step was that anti-tank guns should be fired for training the gunners. There apparently had been a concern to conserve ammunition so that six-pounder gunners had never fired their guns.

Montgomery chose to have his headquarters close to the front. Alexander chose to locate a tactical headquarters near Montgomery's headquarters. The Desert Air Force headquarters was also near where Montgomery chose to locate his headquarters. Since Montgomery expected an attack by Rommel's forces quite soon, he got control of the 44th Division, which he put on Alam el Halfa Ridge. Montgomery asked Alexander if he could have General Horrocks in Egypt to command XIII Corps. General Lumsden eventually commanded X Corps. When Churchill returned to Egypt, he was happy with the way that his changes had affected the organization. This is based on the account in Vol. III Of the Australian Official History.