This is a really good question and wish i had an answer.
My experience with VWs had gotten to the point where i could take any apart and put them back together from memory.
(Plus, they're really simple cars).
With those it's especially needed because every one has been fettled by previous owners.
I've gotten to where we have transaxles in one area, cylinder heads in another, etc.
Because this is my first American car to be going clear through it,
And it had been taken apart and messed up by a PO,
To know how things are supposed to go is by having another car to look at.
And by bugging all of you fine gentlemen of course...

Recently having gone clear through a Fiat for the first time, (and last!

) I got to re-learn the art of keeping track.
Meticulous disassembly becomes a KEY part of complete restoration.
Maybe the most important part?
Like Walt said, take pictures as you go and put them in folders.
Doesn't do any good if you can't find your pics!
I bag all of the hardware in either freezer baggies or regular sandwich bags.
Because the bags will get re-used i don't write on them.
Will take a piece of masking tape, fold it in half, write what's in there and slip it in the bag.
With totes I'll stick a piece of tape on the side that faces out.
Some of those bigger totes get multiple labels.
The masking tape can be pulled and recreated as contents change.
Since storage is so limited, I'm stuck putting things in the attic now.
In order to make that less-nightmarish, I've taken to cutting down boxes.
Constantly going around in alleys behind the mall digging in the cardboard dumpster...

Having a selection of carboard boxes makes it so i can find one with the right footprint for what I'm storing.
It'll get whatever parts, plus fasteners in a baggie, then cut down to be as shallow as practical.
Then the contents written on a couple of sides.
Nothing wastes as much space or makes for struggle in a cramped dark attic as a too-deep box with the four flappy top flaps in the way!

Properly squirrelling of things away is super, super important.
Like has been said, haphazard disassembly is the #1 curse of a car project.
When you're dealing with dirty parts and stuck bolts and cleaning,
The last thing you want to be doing is fiddling with a million pics and making labels and boxes.
As for keeping track, that's another art, but not entirely separate.
With my "disassembly box" method, a sub-assembly's box will become its own 'staging area'.
Ideally, only clean parts will go into the box.
It'll sit somewhere more front/center, as fasteners get wire-wheeled, things get blasted/primed/painted.
New parts like gaskets or fasteners will be included.
getting on to this part early is good if some things are hard to find.
Or especially if you get sent crappy parts and have to try again.
If something is going off to a specialist, the box can be sitting ready to receive the new part.
Often, I'll see the box and label and it will remind me that i have to call that guy!
Eventually, everything needed will end up in the box and it can live in the deep/dark corner of the attic.
Once the car is painted, at assembly that part comes back out, it's all ready to just be bolted on.
My biggest problem on a multi-year, good-God-what-have-i-done extensive/expensive complete resto is buying multiples.
That black car took over ten years and I had gotten two or three examples of certain hard-to-find parts by the time it came together.
I forget what I got! Forgot that i got what i wanted already...! Getting old sucks!
If i'm going to put a certain project down the road, like say what I'm doing now with heater blower or wiper assemblies,
I'll get the new parts that i can easily, then box it, but set it aside closer rather than farther.
Golden rule is that ANY TIME a new small part comes in - fastener, gasket, grommet, whatever.
It HAS to go into the correct box.
If you take, say, wiper mount bolts out of their box/baggie to wire-wheel or compare or buy grommets, they have to go back.
It cannot must not just be "set down" somewhere, otherwise it's GONE!
My shop area, it has so many projects going (or stalled out

) that if anything just gets set somewhere, it's gone.
Don't even bother getting something if it's not going into its box...
For a while i had a big wipe-board in the shop and was trying to keep track that way,
But it wasn't handy enough and i always forgot to update it.
Lots of times I'll make a contact in my phone, say "wiper assembly",
I can take notes and put them there, say when I'm way up under the hood,
But also use those same notes later to look up stuff when I'm on the computer in the house.
Also can look at pics i took of part numbers or whatever and move them to the contact notes.
Having a smartphone in your pocket is like cheating compared to the old days, eh?
I have an iphone, made of glass(!) but use a 'Lifeproof' brand case, so it can survive being dropped a dozen times a day.
It also is soft enough, that it's easily held between your teeth when working with your hands full.
End up using that thing to take pictures of stuff that's hidden or too dark to see.
Used to carry a flashlight, now just the phone.
People laugh when they see my battered phone case,
Covered in teeth marks and overspray...
But i get my cars back together in the end!