Best practice for filtering and categorization?

I’m a heavy user of Gmail labels; I have hundreds. I’m trying to migrate away from the Gmail web console, and so far Mailspring has handled the labels 99% of what I expect, so I’m very impressed with that.

I’ve experimented enough with migrating to desktop clients over the years to understand that Gmail implements their “folders” in a non-standard manner, in a way that caused problems for desktop clients for a long time. I’d like to know what the community/official recommendation is for managing abstract rules that auto-categorize my mail and get it out of the uncategorized inbox. Should I continue to manage my filters within Gmail, or should I start to learn the Mailspring techniques and make use of (I think) “Mailbox Rules”? Are there any gotchas that I need to be aware of that might disrupt the way that my Gmail inbox has always worked?

Thank you.