Thus, what Stephen is actually perceiving as he looks around Sandymount Strand is just a signature and not at all the thing itself. For Stephen, this is tied to the first idea because, in the case of vision, form is opposed to substance.
When Stephen then thinks of "Signatures of all things" he is thinking of the philosophy of the German mystic Jakob Boehme who maintained that a thing can only be encountered through its opposite. Vision is unique, then, because what we perceive (the form) and what exists (the substance) are distinct. According to Aristotle, this is different than sound, for example, because in sound some of the substance gets mixed up with the pure form in the process of hearing. We see just a pure form, but the substance – the thing out in the world – is entirely separate. Let's look at just the first paragraph as an example: The opening: "Ineluctable modality of the visible" alludes to the Aristotelian idea that when we look at something, the thing itself is not part of what we see.
The difficulty now is just following his train of thought, which can often turn on references that the average reader doesn't know much about. Now, in "Proteus," the trouble isn't determining the external from the internal or deciding who is talking because it's all Stephen. In extreme cases, the two can become indistinguishable. This may be a silly example, but knowing how self-absorbed Stephen is we can realize that he's constantly faced with the mad-rush of his own thoughts and external reality going on at the same time. You have trouble distinguishing the external world – what's actually out there – from the internal world – what's just going on in your head. Since your ex is supposed to be sorry that they left you and secretly sad, you project your desire to have them seem sad onto the scene and imagine, for instance, a little bit of sadness in their voice that may or may not be there. You're trying to be objective about it, but you can't help emphasizing certain things about the scene as a result of your subjective prejudice. Afterward you are trying to determine whether or not they seemed happy. Your girlfriend or boyfriend just broke up with you and you have coffee. But this isn't just difficulty for the sake of difficulty. "And then Stephen thought, in a free-wheeling manner based largely upon puns." As a result, it is hard to distinguish the dialogue and the action of the scene from Stephen's own interior thoughts. There isn't any introductory phrase announcing this as interior monologue, e.g. What makes the first two sections of Ulysses difficult is the sudden un-announced turn, a few pages in, to Stephen's stream-of-consciousness. First, let's reflect on how far we've come. First of all, Don't Panic! Later parts of the book again become easier, and you can't be expected to get too much out of "Proteus" on a first or even a second read. The first two sections of Ulysses are by no means easy, but this one steps it up a notch.