Generally, you want to "match-mark" any rotating parts to make sure they stay in balance (such as removing a flexplate or flywheel, or unbolting a torque converter from a flexplate or a clutch from a flywheel.)
Theoretically, this isn't necessary anymore, it's more of an "old mechanic's thing" (because it used to be,) or something still put in the manuals out of habit. If you don't, no need to worry much about it.
(And, for engines that are timed using trigger notches on the flywheel/flexplate, one hole will be slightly "off-pattern," which will "key" the flexplate into a single orientation anyhow.)
Match-marking is easy enough - I usually remove the first screw, then give the hole a quick hit with a bright colour of spray paint. It dries while I'm working, and then I have a screw hole and spot on the flange marked with white/yellow/bright red/bright blue/whatever to line back up visually - saving me the trouble of keying something in.
Ditto when servicing Cardan joints - clean a spot on each yoke, and mark with a bright colour of paint. When aligning the parts around the new joint, simply line everything up.
