I've got a question about Trash/Drafts/Sent folders. By default when I created mailboxes via ISPManager panel, it wast Inbox.Sent, Inbox.Trash, Inbox.Drafts. which I didn't like because having sent and drafts as subfolder to inbox was kinda lame imo. I wanted those 3 to be as separate folders, not as subfolders. Creating them was no problem, just .Sent (for example) in maildir and clients can see it. The questions, how I "make" server to know that it should now send deleted mail to .Trash instead of .Inbox.trash, drafts and sent to their new fodlers respectively.
Except for INBOX, these folder names aren't special to Dovecot. It doesn't know or care what they're called or even whether or not they exist. You used a tool which created a default set of folders and then you renamed three of them, and that's fine with Dovecot.
It's IMAP clients you need to worry about, not Dovecot. By convention (and only by convention), IMAP clients store drafts in a folder called "Drafts", deleted mail in a folder called "Trash", and sent mail... well, for sent mail there's not much of a convention. Most IMAP clients use "Sent", others use "Sent Messages", others use another name. For most clients (e.g. Thunderbird), these are just the defaults, and it's possible to configure the client to designate a different folder as the drafts, sent, or trash folder.
I think it's good that you renamed them from "Inbox.Trash" and so on to just "Trash", because that will be a better match for what most IMAP clients will use by default.
Again, except for INBOX, the only way Dovecot will treat any folders differently from others is if you've configured it to do so. One common configuration is to configure the Dovecot expiry plugin to expire messages more aggressively in Trash. The quota plugins are another place Dovecot might have folder-specific configuration. If you have such folder-specific configuration on your Dovecot server, you can just change the folder names in that configuration. If those folder names don't appear anywhere in your Dovecot configuration, they're not special to Dovecot.