I agree it is confusing, and same with the logistics pipes. It took me a while to figure out that each side is separately up/down, and this isn't really indicated anywhere.
It is intuitive to assume the loaders direction dictates how the resources are moved around, but any deviation from default factorio behavior needs to be managed by code.
And right now, that code doesn't exist.
That's why you're getting confused, and i'm sure many other people are too.
I made a discord for warptorio if you want to talk a bit more easily.
https://discord.gg/a9CNarA