My method for reading it, (or so I hope), will be to read it through, resigned to not understanding a lot of it, hopefully to enjoy it in spite of this ignorance, and to then revisit each section with some annotations to help me...
But let's say you take the Proteus section - which is Stephen's inner monologue. If you were to be able to read another person's thoughts, you'd not understand much of what they were thinking about. Especially if they were the sort of muddleheaded intellectual/aesthete that Stephen is supposed to be. In other words, while you can find out what is going on by consulting academic notes, you're not really necessarily SUPPOSED to understand it.