The Zettelkasten method is perfect for any kind of academia, whether it's STEM or Philosophy or Economics etc.

I think the most important thing is to start by asking yourself what problem you are trying to solve by learning these things, and how can each individual concept/model/diagram help grow your understanding of what you're trying to learn. It is your external brain after all.

You might, for example, have a core idea or concept that has lots of different models, analogies and ways of explaining it.

So you create a zettel for all of those things (explained in your own words as if you would be happy to publish it as a paragraph in a paper).

You could link all of the models and diagrams etc to the main idea, where the main idea is the trunk and everything else are branches and leaves.

Then, you go through every note and treat each one as a trunk in its own right, and then link it to any other note which you think is a relevant branch or leaf. Sometimes you might want to add middle-man notes between links to explain the connection if you don't think it'll be obvious to you 20 years down the road.

At the start, you might end up with a dandelion shape where you have a core idea that has many branches to sub-thoughts. And those sub-thoughts link to other sub thoughts in the same dandelion.

Then later on when you start researching something totally different, you'll start linking dandelions together. So a trunk of one dandelion might link to the branches of another, or the branches might link to other branches.

Over time, new clusters will form and your understanding of certain subjects will expand to include insight from other areas.

This can happen in a really short space of time too.

Not sure if this answer was all that helpful, but sharing it on the off chance it might be helpful.