I have found that using your Arc as your notes outline helps you keep track of both what happened and what was expected and didn't happen.
Depending on what I'm doing I often think of a scene or scenes that might involve the players and then plot up to that point and after it, depending on what seems logical.
Lately I have a word pad with some notes and/or maps on it with locations, important NPCs, and sometimes player hand outs to help.
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I'm actually planning to go analog in my next campaign while at the table - prepping monster stat blocks and the like beforehand and focusing on making noted of player choices and decisions at the table in ye olde wire-bound notebook. I found that too many electronics at the table, especially to try and make notes of what was going on, led to me trying to keep it all on the computer and I spent more time managing my tools than managing the game.
Two things have recently helped my campaign prep immensely.
1: Spreadsheets: Being able to have parties of humanoids, monsters, or even the party spread out on a single piece of paper is amazingly useful. While not feasible with every monster due to their own special rules, this can help you really do some solid planning.
2: passive rolls: I keep these in place even during pathfinder, unless a character tells me they are making a roll I assume they are taking 10 on everything. I only roll opposed checks if both sides are actively attempting to thwart one another. I keep track of these also with spreadsheets, where I also write down things like situational modifiers and other important bonuses.
It takes a bit of work to set things up, but g~%#+*n is my campaign more immersive with the players rolling fewer skills and their passive skills mattering more than their ability to roll well.
I can't focus on reading PDFs in a non-work context for some reason, so all my games are run with physical books and prodigious use of post-it notes, though I pull up monster stats online on the d20psfrd (easier than flipping through all the bestiaries for me). If I'm creating an extra encounter/adventure, I'll usually write it down in a notebook, though I'll use a Word document for extensive NPC stats that I'm creating.
If you're running a "West Marches" sort of game making a note before and after what sorts of plot changes the NPC interactions may have with your main characters is a bit useless. Likewise there's pre-prep for party cohesion that I would normally recommend, but if you're running a Paizo AP that already takes that into account again it's not very useful.
In general, I find railroad-style games require fewer notes than sandbox games to get started, but after awhile, the sandbox-style games only need a few reminder post-its / 3x5's or random notes on NPC character sheets.
For general ease of play, I try to print copies of my monster stats and a general sketch of how the monsters may be pre-positioned for faster map set-up. If any have any strange abilities (or worse, odd templates) - I try to go over those with a highlighter so I don't accidentally read over it (which is generally less of an issue if I'm the one who created the NPCs, to be fair). If there are items or effects which the PCs will have access to or be afflicted by that may last the entire session, I try to put those on a 3x5 card so that I can just hand that to the affected player(s) for quick reference and to cut down on game-time of folks having to look them up.
Condition Cards and Spell Effect cards are also life-savers on time saving / reminders. If they're currently sold out or you're not able to get them for whatever reason, again 3x5 cards are a life-saver.
Initiative and remembering initiative order can also be a pain - and also solved by 3x5's. I usually have my PCs write down their character name in the center of a 3x5 card and their initiative modifier on the top left. If it's a game where specific skills will likely come up often I may have them add those skill modifiers under their character name (most often their Perception &/or Sense Motive). For initiative I have similar (usually more generic cards) for my monsters so that I can just stack them in initiative order - removing cards for characters on delay or readied actions and returning them to the stack when their turn comes in.
What I (currently) do:
Read the material
Extract images of scenes/NPCs from PDF to a laptop for show & tell
Make a "cheat sheet" with essential PC stats (Perception/Sense Motive)
Transpose any "template" NPC statblocks to minimize page flipping
Re-read the material
Re-read the material
Re-read the material