There is no right or wrong, as long as it gets the amp back together correctly.
First, do all the wires really need to come off? Instead of completely removing a circuit board to replace a part, I generally try to just free it from its mounts and flip it over enough to get at the solder side, wires still attached. Sometimes tipping the amp on its face helps. The amp doesn't always have to face the same way during repair.
But if you must, like pulling the output transistor board on a large PV power amp, I usually make a outline drawing of the board with a few landmarks added, then I draw lines from each spot on the board with a wire and what color wire it is.
Masking tape is easy to make flags with, wrap a piece around a wire and stick it to itself. It takes pen ink readily so you can write on it, and it is easy to remove by tearing. SO I can tag a wire with a post number or whatever it goes to.
Cables are often made with different size connectors so you can't hook it up wrong. But when that is not true, if I have two identical connectors with say 6 wires each. I get out a Sharpie marker and blacken one side of the connector, and also the same side of its mate. SO the plain white one goes to the plain white jack, and the one with the black line goes to the jack with the black line. More than one pair? OK one plain set, one set with one black spot, another set with two black spots. And like that.
Sometimes there may be more than one wire of a color. But if I have a black and blue next to each other, and a black and red over yonder, I can tape the two pairs together, eliminating the confusion over which black wire went with which color wires.
Marshall transformer? Most times I demount the old one and leave the wires on it. I mount th new one, and transfer wires over one at a time. Can't screw that up easily. Otherwize a square drawn on paper with tabs where the wires go allows me to draw in lines for red, brown, pink whatever, so I can put them right.
And sometimes I use knots. If I am in back of a speaker cab from a PA stack, I might have a half dozen wires coming down to the crossover from a hole in the filler stuffing. Again with the multiple black wires. I can put a knot in the end of one wire to mark it from the other same color. Of if I know they are pairs, I can knot two wires together. Just a simple overhand knot.