What’s confusing about wine prefixes apart from the fact that wine itself doesn’t come with a graphical interface to manage them? On a Deck, Steam should handle these for you
Calling them “prefixes” is about the total of the confusion. Call them “instances” or even just “boxes” and it’s suddenly clear what they do.
(The only reason I’m not using “sandbox” is because they don’t really provide sandboxing from a security point of view, only a kind of separate instance with its own configuration but with access to everything via the Z drive)
Once you figure out that using a different “wine prefix” only really means a separate “Windows” with it’s own config and file structure there’s nothing confusing about it.