Your scripting method...
It's no different to using a script editor. You're still using commands, only you're typing them into Notepad.
The commands you're using seem to be those that Pokescript use. XSE uses slightly different commands like #dynamic and so on, which is why they seem confusing to you.
Otherwise, it's the same basic idea, you type commands in the order you want them to happen in-game.
I wholeheartedly recommend learning to use XSE- so little people use Pokescript nowadays, if you ever run into problems you're more likely to get quicker help if you're using XSE. It's really not that tricky- I'm no master at it myself, but I tend to be a bit slow, and since you seem to have Pokescript down I don't think it should be a problem for you.
Just my two cents :)