HomeKit has a hierarchical structure to organizing devices and provides a couple of additional options to manage dozens of devices.
The basic HomeKit organizational structure is Home > Room > Devices. HomeKit provides support for having control of more than one home, so the top level is the home. Each home is then divided into rooms. And finally the devices you are controlling and placed into rooms.
Creating Rooms in HomeKit can be trickier than you think. How do you handle open floor plans? How do you handle entry ways that aren't really rooms, but are connected to three different rooms? Where do you put a staircase that opens into the living room on one floor and into the library on another floor? How do you handle hallways? Do you really want to create two rooms to handle the front and back porch? The good news is that there is no right or wrong way to organize your rooms—do whatever works best for you, and if you change your mind later on, it is easy to change and create new rooms and move your devices around accordingly.
For example, my house has four different staircases. For each staircase, I have to decide which room to put it in. This might be the room that you most often think of the staircase in, but it can be complicated: sometimes a single room may have two staircases attached; sometimes the staircase doesn't have a dominant room, or maybe it is attached to entry ways and hallways that don't warrant having their own room.
Being that a room determines when you will see a device in HomeKit, if you want to see the status of the staircase lights with the other living room devices, you might want to assign the staircase to the living room. Alternatively, you might not want to see the stairs while viewing the other living room devices (or maybe you don't want the staircase lights to go on when you tell Siri to turn on the living room lights). In this case, you could create a "room" called "Staircase", and place all of the staircases into that "room". Then you can also turn on all of the staircase lights in the home by saying "Hey Siri, turn on the Stairway lights". Entryways are another candidate for this type of organization.
Zones and Groups
HomeKit also provides for two additional organizational units:
Zones: Zones are used to group rooms into additional organizational groupings, such as: Inside/Outside, Upstairs/Downstairs, Bedrooms/Bathrooms
Groups: Groups are used to group devices into organizational groupings. An example of this would be if you have five smart bulbs in a chandelier, and you want to control them as one virtual "light".
Rooms can belong to more than one zone. For example, you can have a zone called "Upstairs" and place all of the upstairs rooms into that zone. You could then have a zone called "Bedrooms" and place all of the bedrooms into that zone. The "Master Bedroom" can be a member of both the Upstairs and the Bedrooms zones.
You can also use zones to create an alias, or an alternate name for a room. For example, you could have a room called "Home Theater" and place it in zones called "Game Room", "Family Room", "Entertainment Room", and "Movie Room". Or you could have a bedroom called "Tim's Bedroom" and place it in zones called "Kids Room", "Boys Room", and "Timmy's Room".
One of the deciding factors on whether to use a Zone or a Room, is that you can't select or view a zone in the Home app, you can only address a zone using Siri. Rooms can be viewed and are used to visually organize devices throughout the Home app. So how you want to see the device will determine which room to place it in, and how you want to refer to a device can be a good use of a zone.
Once rooms are grouped into zones, you can use Siri to control all of the devices in the zone. For example, "Hey Siri, turn on the Upstairs lights".
Only similar types of devices can be grouped together (for example, lights can be grouped with other lights, and outlets can be grouped with other outlets).
Use groups to group any devices you want to control as one, such as all of the bulbs in a light fixture, or if you have multiple can lights in the kitchen and want to control them all as one unit, or all of the outlets that turn on your holiday lights.
Once devices are grouped, they cannot be controlled independently from Apple's Home app, but they can in 3rd party apps like Home+..
The on/off state, brightness level, and color will be set for all devices by controlling the group.
To place a device in more than one group, you will need a 3rd party app like Home+.
Other Organization Methods
Scenes aren't really an organizational structure in HomeKit, but HomeKit Scenes allow you to setup a bunch of devices just like you want them, and then turn them all on or off with the touch of a button or through an automation. Here are some examples of HomeKit Scenes:
Up to Bed: Turn all of the staircase and hallway lights from the basement to the bedrooms to 75% to light a pathway from the basement family room to the bedrooms
Goodnight: Turn off all the lights, and lock all the doors
Watch TV: Dim the living room lights and turn on the TV
Holiday Lights: Turn on the Christmas tree lights, the holiday lights, and the outdoor holiday lights
Party: Turn all the lights to 80% and shuffle your party playlist on all of your HomePods
Each HomeKit device (and Scene) can be set as Favorite, which means that in addition to appearing in the device's assigned room, it will also appear on the Home app's main "Home" screen. You can control the order that devices are listed using the home screens Edit button.To keep your home screen from being cluttered, only place your favorite devices and scenes on the home screen (by default any new device you add is set as a favorite). Remember that you can quickly tap on the summary at the top of the Home page to view any device that is on, and the status of all sensors, regardless of whether it is favorited or not.
Also see the Device Names & Siri Interactions article.