I'm playing Witcher 3 right now, and I have a few presets downloaded, and all the ini's in the correct folder. The problem is that in their respective readme files they have customized shaders which need to be pasted into the reshade-shaders folder. I am wondering if I need to be worried about overwriting, or is there a way to have each preset load their own shaders from a sub-folder so switching between many presets in-game doesn't require me to copy the shaders over every time I want to switch.

I don't switch presets often, but just curious if this is something that matters, and am I missing something here?

As long as the presets just add new shaders, there is no problem. It they modify existing ones that are in use by a different preset, then that might be a problem. Just try it.
No, shader search paths are not bound to a preset (since they are unique to the user).