i would focus on just taking notes on related topics, without much structure for a bit. try to link them together if they are on related ideas a bit. once you have a network of notes that feels a little less manageable (~100), i create a "map of content" where i link to all notes related to that concept, and in it i essentially tell a higher level story about how those notes relate to each other.
I also find it easier to read certain philosophers than others because they themselves seem to be empathetic in the way they write their thinking. Almost as if they know that they could be wrong about the conclusions they're coming to, and that the truths they uncover aren't necessarily absolutes but instead, at least to a certain degree, subjective and personal.
Reading phenomenology for instance doesn't get me feeling like the author is self-indulgent. I find it easier to empathize with the philosopher because the philosopher is trying to empathize with me.