If this is a modern engine, it’s pretty dang hard to screw up since everything pretty much lays in place and has dedicated ends.
Um, well... a friend of mine once helped me remove and replace an engine, and he somehow managed to mix up several connectors on "his" side of the engine. Fortunately, the connectors didn't actually connect and he didn't force them, so he just left them hanging and badly misrouted but didn't say anything. It was getting really late and cold, so we left it for the time being.
About five minutes after he went home I figured it out.
Lesson learned... double-check each other's work. Ask the other guy to check your work as well, and no one will get offended.
Here's what I use.
https://www.arromark.com/products/pm-16
It't a liquid paint that they use at places like PickNPull that has a valve actuated tip to keep the paint from leaking or drying out.
Yep, I've had the best luck with paint markers. Oftentimes if there's potential confusion, I'll make symbols instead of trying to write a description. Like one has three lines, one has a circle, another has a triangle, etc; things that would be easy to tell apart even if they rub off partially.
Of course, flagging with masking tape works fine, too, and allows you to make notes like "route UNDER radiator hose".
Paint markers always seem to dry out really fast. I also keep a few bottles of cheap fingernail polish on hand for marking stuff.