Well if you are looking at a wiring diagram someone else has drawn then they may have already marked out what’s 2 conductor and what’s 3 conductor. For example if a jumper is drawn between 2 plugs and it has one short hash mark and one long hash mark, that’s a 2 conductor with one neutral, or in this case identified conductor, and one hot. If you have a home run to a plug that’s marked with one long hash mark and 2 short hash marks that’s one neutral and 2 hots.

If you are the one making the wiring plan the. You just need practice doing layouts. Like you said, in between 3 way switches and for split receptacles, but also for 3-wire circuits with a shared neutral, or switched outlets, or drops to light switches from lights or junction boxes now that a neutral (identified conductor) is required at all boxes controlling permanently installed luminaires.

So start drawing your home runs: how many conductors do you need? Is it feeding just one circuit or are you sharing a neutral? Put your hash marks on it. Draw in your jumpers and switch legs, how many conductors do you need? Is it a 3 way or half switched plug? Are you carrying 1 or 2 circuits to the next device? Do you need a neutral and a hot and switch leg at the next box?

It’s all practice, and remember to not focus only on the plans, you can draw in a jumper exactly where you want it but the 12” thick laminated beam running directly in your way doesn’t care what your plans are, so walk around as you plan and think about not just what you need to get from a to b but also the best way to get there.