How to manage the configuration

I'm relatively new to HA, but in the last few weeks I've created a number of setups (lights, heating, aircon and others) and the list of quickly growing. By now the list of helpers is a few pages long and the same can be said about the automations as well.
I realised I'm starting to lose track of what's where and what belongs to what. I tried to keep some sane naming conventions, but even with that I ended up with 10 different automations that turn various plugs or lights on or off. I would like to somehow group all the resources (some of them created via the UI, some in configuration.yaml) that are related for example to 'lights in the lounge' or 'power consumption' or 'heating in bedroom 1'.

What's the best way of doing that?
Also - is there a way to visualise all the integrations (both actual and helpers) and automations that relate to each other?

That's what labels and areas are for. You can use multiple labels on one device and/or automation and/or scripts, etc. In this regard, you can label all your lights as Lights, but then also add another label for the specific rooms they're in, as well as a label for the type of protocol they use (WiFi, Zigbee, Zwave?), and on and on and on and on.

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Retrospective planning is hard. Often going back to basics and doing it again, based on experience may be more efficient.

By browsing various blueprints I realised that I can simplify my automation significantly by using the choose actions with a number of condition statement. That has reduced the sheer number of automations significantly. Now I can have a single automation to manage all light trigger/actions or aircon.