Whatever method is open to you at the time. You don't attack a person a certain way just because it does more damage. You use whichever method will actually work against them, and scale up your damage efforts from there.
Typically Bayman has a harder time getting in, so in the early part of the round you want to use enders that will allow you to continue pressure. During the later part of the round, after you've taken 50% lifebar, is when you want to start thinking about using the large damage finishers.
This is only the standard rulebook for a general intelligent opponent though. Every player is going to react differently to the options you use. Sometimes, if a person is going to just keep holding no matter what, maybe you WANT to hit them with a bunch of back breakers. For a person who likes to hit buttons, you want to keep looping them with bounces and wall advantage setups. For a cautious, high level opponent, going by the playbook may be a more solid approach.
The very first time you stun somebody you should be trying to gauge how they respond and making an informed decision about how you will proceed against them. If they are inclined to hold, you can punish that in a very big way. You are never obligated to throw them, nor are you ever obligated to launch them. You can OH them at the end of a stun too, or delay any of these options for further mixup. Find out what works and identify it early on. It's different for every person.
As far as neutral game goes, its entirely matchup based. But a good place to start is with a few general rules. If you think you can catch them running in on you, stop them with
. If you think you can make them whiff in a big way, punish that with
. Some characters like Hayate can't really be stopped easily in either way and you have to get more creative, or space much further out. Not every fight is going to be easy.