Photos and notes are your friend.
When I fixed the engine in my truck I'd take a photo or series of photos, then sketch a diagram using tape and a marker to label each part and connection to match the sketch. Just about every part, tube, wire, pipe or bolt had a name and label. I had a notebook full of descriptions, some with photos, others with photocopied pages from my FSM.
I also went through a box of Ziplock bags with post-it notes describing specific bolts and parts that weren't obvious. Don't assume that anything is going to be obvious when you have a hundred pieces laying around your garage. You can pick out a water pump, but you'll sure as the sun rises forget the order of the bolts that go around it. A bag of bolts just looks like a bag of bolts, but a little note that just says "front right engine mount" helps a whole lot. Or if the bolts are different lengths and it's critical (like those on the timing cover, water pump and oil pump on a 22R) I numbered each of them to match a diagram.
You can see the tables and some of the parts I had laid out doing this.
You can paralyze yourself worrying about it so you just need to dive in and start. But don't do it with some organization.