Fundamentally, maps were made in World War II the same way they had been for a couple of hundred years, by starting with a geodetic survey to establish a triangulation framework, then adding topographical detail. Existing maps would be used as a basis if available; if there were none, and physical survey was not an option, air surveys were possible, though specific photography was required for accurate map-making (straight runs, overlapping shots and no tilt, slightly different requirements compared to intelligence gathering missions). As well as central operations there were units deployed in the field for the rapid creation and dissemination of maps such as US Engineer Topographic Battalions and Royal Engineer Field Survey Companies, the latter divided into sections of surveyors, drawing sections to produce or revise maps, and printing sections with mobile presses.

The mapping operations for the D-Day landings are a good case study, if not entirely representative of the wider war; "the greatest mapping project ever" as described in an article from The American Surveyor. The RAF flew 342 sorties to produce photographs for 1/25,000 scale maps, the Inter-Services Topographic Department amassed details on tides and possible invasion beaches, partly from extremely low level reconnaissance flights but also from any other material that could be obtained including pre-war holiday brochures, and holiday snaps and postcards procured from the public by an appeal on the BBC. Amphibious operations required nautical charts in addition to land mapping, and a combination of the two for e.g. naval bombardment of land targets, so clandestine hydrographic survey missions were carried out, including taking sand samples from beaches; geological information was important for determining where tanks could be landed and sites for the Mulberry harbours.

The "Historic" section of the Defence Surveyor's Association website has some pertinent information, most notably the official British history Maps and Survey by Brigadier Archie Clough. Unfortunately there isn't very much in there about the Pacific theatre, but there is a short section in Chapter XII, and coverage of Australian operations in the region in Chapter XIII.

Australian Bathurst class ships were fitted out to conduct surveys for the purposes of conducting mapping operations in the Pacific. Notable examples were HMAS Benalla and HMAS Shepparton. There is also this book, which is relevant, if you can get your hands on it.