The Map room basically was it.

At the time the Pentagon was still under construction, while the Navy was still using the "Main Navy" building where the Vietnam Memorial is today. While Admiral Leahy in his role as Chief of Staff to the Commander in Chief was along with the others constantly in and out of the WH and FDR made sure the Map Room was kept up to date, while other key decisions and meetings were also held in the Yellow Oval Room that he used as a study on the second floor.

The fact is that the War and Navy departments were not very good at acting jointly at the top until WW2 forced them together, meaning that one giant room where they both laid all the cards on the table was a tough sell short of the President as that was the only person they both answered to.

While much of the strategic planning was also done at the series of conferences. Acadia, Casablanca, Yalta, and the various Washington conferences were the best times when the Combined Chiefs of Staff from the US and UK could gather mostly in one place and debate proposals and formulate plans.