Even though I'm using an older form of command-control, I'm still dividing each area into blocks, and wiring each block individually from the area's panel. This way, if I want to add detection or control-panel signalling later, it (should) be easier. I've decided to protect groups of blocks with 1156 automotive lamps, as several have suggested, so the panels and blocks let me lay that wiring out as well.
The panels themselves are sheets of plywood hanging under the benchwork, but hinged so that when I'm not working on wiring they can fold up under the layout. I really need the storage area under the layout, and this will keep the area under the panels more open, so I can get at stuff stored there w/o having to reach around behind the panels.