Much of engineering is simply organization, techniques for making improbably large problems manageable. At its best, engineering is an art. Mostly, it's just drudgery. But drudgery, wielded by artists, let men walk on the moon.
You care because you work on cars. Suppose you're not different than everybody else and the super-talented paint and body artiste to whom you entrust your car turns out to be a little flaky. Your project is with him for a year and a half. When you get it back, those boxes full of hardware that seemed so obvious in its application when removed might as well be for the Millenium Falcon.
The solution is to bag and tag. Imagine if, when you wanted to reinstall the right rear suspension, you had a Ziploc(r) bag full of hardware that said "right rear suspension." You could figure out which fasteners went where. The same for the intake manifold, trunk lid and taillights. That would be pretty cool. You would be a genius with awesome powers of foresight. And you would spend a lot more time putting your car back together than sorting through a box of bolts for one that looked right. As a bonus, Ziploc bags offer dry, dustless storage even in damp conditions. The bags can be thrown together in a box without being scrambled. My favorite kind are the freezer bags with writing panels.
The reassembly process would be even easier if every connector in the wiring harness and every vacuum hose were labeled. I used to use masking tape and a pen until our local champion of electrical anarchy and mechanical mayhem got all highfalutin and bought a Brother P-Touch label printer. The text is clearer, longer lasting, and all-around more elegant than chicken scratches on masking tape. A heat gun used for heat-shrink tubing will blacken the entire label, but normal underhood temperatures will not. Once stuck, the adhesive is reasonably resistant to brake cleaner. The labels also work well in the event you bought your sockets before large, high-visibility markings became fashionable.
Magnetic parts trays are my third weapon in the battle against chaos. They will stick anywhere and hold hardware, even upside down on the bottom of a car. Their rubber bottoms won't scratch paint but dirt will, so be careful. The trays keep nuts and sockets from falling into the depths of an engine compartment or being kicked under the farthest corner of a workbench. I use them for everything, even lug nuts. They work as a sort of temporary bag system, either as an intermediate step or for shorter tasks. One tray just isn't enough. They go on sale from time to time at Harbor Freight Tools for about $2.50, a price at which one can afford to stock up.
Hopefully, these simple tips will help you get there sooner with whatever your own personal "moonshot" happens to be.